rs7716600

Variant names:

• chr5-44874903-A-C
• rs7716600

Your query was ambiguous. Multiple possible variants found:

• chr5-44874903-A-C
• chr5-44874903-A-G
• chr5-44874903-A-T

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 0.773 in 151,576 control chromosomes in the GnomAD database, including 45,742 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 0.77 (45742 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.774 AC: 117166 AN: 151460 Hom.: 45705 Cov.: 30

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.773 AC: 117242 AN: 151576 Hom.: 45742 Cov.: 30 AF XY: 0.768 AC XY: 56870 AN XY: 74046

African (AFR) AF: 0.828 AC: 34250 AN: 41362

American (AMR) AF: 0.704 AC: 10730 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2872 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2661 AN: 5148

South Asian (SAS) AF: 0.721 AC: 3458 AN: 4798

European-Finnish (FIN) AF: 0.766 AC: 8040 AN: 10490

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.778 AC: 52732 AN: 67774

Other (OTH) AF: 0.750 AC: 1575 AN: 2100

Alfa AF: 0.774 Hom.: 156590

Bravo AF: 0.771

Asia WGS AF: 0.623 AC: 2163 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.16
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs7716600; hg19: chr5-44875005;