4-102630446-A-G

Variant names:

• chr4-102630446-A-G
• rs7665090

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 0.55 in 152,024 control chromosomes in the GnomAD database, including 23,399 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 0.55 (23399 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 82 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.549 AC: 83457 AN: 151906 Hom.: 23362 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.550 AC: 83541 AN: 152024 Hom.: 23399 Cov.: 33 AF XY: 0.548 AC XY: 40724 AN XY: 74290

African (AFR) AF: 0.631 AC: 26176 AN: 41474

American (AMR) AF: 0.616 AC: 9416 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1762 AN: 3464

East Asian (EAS) AF: 0.519 AC: 2683 AN: 5168

South Asian (SAS) AF: 0.453 AC: 2180 AN: 4812

European-Finnish (FIN) AF: 0.471 AC: 4962 AN: 10536

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34505 AN: 67970

Other (OTH) AF: 0.548 AC: 1155 AN: 2108

Alfa AF: 0.520 Hom.: 75068

Bravo AF: 0.567

Asia WGS AF: 0.506 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7665090; hg19: chr4-103551603;