rs7644410

Variant names:

• chr3-30499934-A-G
• rs7644410

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.313 in 151,952 control chromosomes in the GnomAD database, including 7,744 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 0.31 (7744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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: 0.313 AC: 47589 AN: 151834 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.313 AC: 47618 AN: 151952 Hom.: 7744 Cov.: 32 AF XY: 0.313 AC XY: 23257 AN XY: 74274

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.328

Alfa AF: 0.306 Hom.: 1051

Bravo AF: 0.312

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7644410; hg19: chr3-30541426;