rs7712675

Variant names:

• chr5-76842742-T-A
• rs7712675

Your query was ambiguous. Multiple possible variants found:

• chr5-76842742-T-A
• chr5-76842742-T-G

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 0.236 in 151,742 control chromosomes in the GnomAD database, including 9,493 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 0.24 (9493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 3 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 = 0.649 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: 0.236 AC: 35717 AN: 151624 Hom.: 9456 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.236 AC: 35804 AN: 151742 Hom.: 9493 Cov.: 32 AF XY: 0.231 AC XY: 17096 AN XY: 74158

African (AFR) AF: 0.656 AC: 27085 AN: 41306

American (AMR) AF: 0.177 AC: 2693 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3468

East Asian (EAS) AF: 0.0404 AC: 208 AN: 5154

South Asian (SAS) AF: 0.0929 AC: 447 AN: 4814

European-Finnish (FIN) AF: 0.0179 AC: 188 AN: 10530

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.0592 AC: 4024 AN: 67936

Other (OTH) AF: 0.219 AC: 460 AN: 2100

Alfa AF: 0.133 Hom.: 617

Bravo AF: 0.268

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.79
DANN	Benign	0.72
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs7712675; hg19: chr5-76138567;