4-102771986-G-C

Variant names:

• chr4-102771986-G-C
• rs223475

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.579 in 151,916 control chromosomes in the GnomAD database, including 26,870 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (26870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87869 AN: 151798 Hom.: 26826 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.588

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.579 AC: 87968 AN: 151916 Hom.: 26870 Cov.: 32 AF XY: 0.578 AC XY: 42866 AN XY: 74222

African (AFR) AF: 0.791 AC: 32804 AN: 41470

American (AMR) AF: 0.560 AC: 8555 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2665 AN: 5158

South Asian (SAS) AF: 0.503 AC: 2422 AN: 4818

European-Finnish (FIN) AF: 0.471 AC: 4949 AN: 10516

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32850 AN: 67914

Other (OTH) AF: 0.583 AC: 1227 AN: 2106

Alfa AF: 0.528 Hom.: 2560

Bravo AF: 0.596

Asia WGS AF: 0.527 AC: 1829 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs223475; hg19: chr4-103693143;