rs7193943

Positions:

• chr16-31259742-G-A
• chr16-31259742-G-C

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 0.692 in 151,984 control chromosomes in the GnomAD database, including 36,603 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 0.69 (36603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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 = 0.728 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: 0.692 AC: 105115 AN: 151866 Hom.: 36577 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.692 AC: 105185 AN: 151984 Hom.: 36603 Cov.: 31 AF XY: 0.686 AC XY: 50951 AN XY: 74264

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.656

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.730

Alfa AF: 0.702 Hom.: 39465

Bravo AF: 0.703

Asia WGS AF: 0.585 AC: 2033 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	0.21
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7193943; hg19: chr16-31271063;