rs161905

Positions:

• chr3-7819728-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 0.336 in 151,998 control chromosomes in the GnomAD database, including 9,817 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 0.34 (9817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51020 AN: 151880 Hom.: 9809 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.336 AC: 51036 AN: 151998 Hom.: 9817 Cov.: 32 AF XY: 0.335 AC XY: 24881 AN XY: 74282

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.320

Alfa AF: 0.387 Hom.: 2087

Bravo AF: 0.313

Asia WGS AF: 0.321 AC: 1109 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs161905; hg19: chr3-7861415;