rs7524102

Variant names:

• chr1-22371954-A-G
• rs7524102

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 1-22371954-A-G has been identified. The variant allele was found at a cumulative frequency of 0.205 (AC=31,208) in the gnomAD database across 152,186 control chromosomes, including 3,671 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.308. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 76 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 = 0.3077 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

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: 0.205	AC:31172	Hom:3665	AN:152068	Cov:32
GnomAD4 genome	AF: 0.205	AC:31208	Hom:3671	AN:152186	Cov:32
TOPMed (Bravo)	AF: 0.216	AC:57093	Hom:6865	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.185	AC:133306	Hom:13076	AN:720786	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.212	AC:496	Hom:64	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.218	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.150	AC:45	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.217	AC:756	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.187	AC:1351	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.250	AC:44	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.227	AC:27914	Hom:3210	AN:122718	Cov:
Turkish Variome	AF: 0.189	AC:292	Hom:44	AN:1546	Cov:
UK10K	AF: 0.177	AC:1340	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.223	AC:1998	Hom:233	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.44
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.38
GPN-Star LLR	N/A	3.6
GPN-Star score	N/A	-0.58
PhyloP100	Benign	-0.44

Showing 7 of 7 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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs7524102;

hg19: chr1-22698447;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar