rs4804803

Variant names:

• chr19-7747847-A-G
• rs4804803

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The variant 19-7747847-A-G has been identified. The variant allele was found at a cumulative frequency of 0.253 (AC=38,427) in the gnomAD database across 152,040 control chromosomes, including 5,673 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.407. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Variant has been reported in ClinVar as Uncertain Significance (no review stars).

• Frequency: Genomes: 𝑓 0.25 (5673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: protective; risk factor no assertion criteria provided B:1 O:2
• Conservation: PhyloP100: 0.0700
• Publications: 125 publications found

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -12 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4070 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.253	AC:38427	Hom:5678	AN:151922	Cov:32
GnomAD4 genome	AF: 0.253	AC:38427	Hom:5673	AN:152040	Cov:32
TOPMed (Bravo)	AF: 0.258	AC:68184	Hom:10234	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.233	AC:56003	Hom:7337	AN:240710	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.221	AC:517	Hom:63	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0769	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.160	AC:48	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.166	AC:579	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.0540	AC:394	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.250	AC:44	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0413	AC:5055	Hom:119	AN:122426	Cov:
Turkish Variome	AF: 0.180	AC:278	Hom:25	AN:1546	Cov:
UK10K	AF: 0.195	AC:1478	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0767	AC:687	Hom:25	AN:8960	Cov:

Showing 14 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

ClinVar submissions

Significance: protective; risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Dengue fever, protection against (1)
-	-	-	Mycobacterium tuberculosis, susceptibility to (1)
-	-	-	Susceptibility to HIV infection (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.9
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.74
GPN-Star LLR	N/A	3.5
GPN-Star score	N/A	-0.25
PhyloP100	Benign	0.070
PromoterAI	N/A	0.019	Neutral

Showing 8 of 8 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4804803;

hg19: chr19-7812733;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar