rs7710617

Variant names:

• chr5-3073738-G-A
• rs7710617

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 0.108 in 152,050 control chromosomes in the GnomAD database, including 1,490 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 0.11 (1490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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: 0.108 AC: 16417 AN: 151932 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0510

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.108 AC: 16445 AN: 152050 Hom.: 1490 Cov.: 32 AF XY: 0.106 AC XY: 7857 AN XY: 74350

African (AFR) AF: 0.252 AC: 10450 AN: 41402

American (AMR) AF: 0.0671 AC: 1025 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.115 AC: 552 AN: 4812

European-Finnish (FIN) AF: 0.0287 AC: 304 AN: 10592

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0510 AC: 3467 AN: 68000

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.0797 Hom.: 150

Bravo AF: 0.115

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.29
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7710617; hg19: chr5-3073852;