rs7716600

Positions:

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

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 0.773 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.44874903A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.750

Alfa AF: 0.771 Hom.: 102900

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7716600; hg19: chr5-44875005;