rs17395886

Variant names:

• chr4-161358233-C-A
• rs17395886

Your query was ambiguous. Multiple possible variants found:

• chr4-161358233-C-A
• chr4-161358233-C-G
• chr4-161358233-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.121 in 152,060 control chromosomes in the GnomAD database, including 1,475 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 0.12 (1475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 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: 0.122 AC: 18464 AN: 151942 Hom.: 1475 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.121 AC: 18460 AN: 152060 Hom.: 1475 Cov.: 32 AF XY: 0.124 AC XY: 9181 AN XY: 74310

African (AFR) AF: 0.0303 AC: 1256 AN: 41514

American (AMR) AF: 0.153 AC: 2326 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3470

East Asian (EAS) AF: 0.171 AC: 884 AN: 5158

South Asian (SAS) AF: 0.233 AC: 1125 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10586

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10599 AN: 67972

Other (OTH) AF: 0.111 AC: 234 AN: 2108

Alfa AF: 0.138 Hom.: 1220

Bravo AF: 0.117

Asia WGS AF: 0.185 AC: 642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17395886; hg19: chr4-162279385;