rs34548976

Variant names:

• chr7-31032854-C-T
• rs34548976

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 0.387 in 151,952 control chromosomes in the GnomAD database, including 12,497 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 0.39 (12497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.387 AC: 58791 AN: 151834 Hom.: 12473 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.387 AC: 58851 AN: 151952 Hom.: 12497 Cov.: 32 AF XY: 0.384 AC XY: 28548 AN XY: 74274

African (AFR) AF: 0.557 AC: 23051 AN: 41420

American (AMR) AF: 0.301 AC: 4599 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3468

East Asian (EAS) AF: 0.102 AC: 528 AN: 5156

South Asian (SAS) AF: 0.357 AC: 1717 AN: 4804

European-Finnish (FIN) AF: 0.356 AC: 3755 AN: 10554

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22780 AN: 67964

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.347 Hom.: 15094

Bravo AF: 0.393

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs34548976; hg19: chr7-31072469;