chr3-161675181-G-A

Position:

• chr3-161675181-G-A

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 0.903 in 152,252 control chromosomes in the GnomAD database, including 62,231 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 0.90 (62231 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.161675181G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288087	ENST00000665274.1	n.116-59261G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137342 AN: 152132 Hom.: 62163 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.903 AC: 137471 AN: 152252 Hom.: 62231 Cov.: 32 AF XY: 0.908 AC XY: 67581 AN XY: 74424

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.870

Alfa AF: 0.884 Hom.: 7438

Bravo AF: 0.902

Asia WGS AF: 0.981 AC: 3412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2404571; hg19: chr3-161392969;