rs34548976

chr7-31032854-C-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 0.387 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.363

Alfa AF: 0.347 Hom.: 1972

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34548976; hg19: chr7-31072469;