rs161905

Variant names:

• chr3-7819728-C-T
• rs161905

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;