rs6861611

Variant names:

• chr5-170136579-G-A
• rs6861611

Your query was ambiguous. Multiple possible variants found:

• chr5-170136579-G-A
• chr5-170136579-G-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 0.164 in 152,124 control chromosomes in the GnomAD database, including 2,188 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 0.16 (2188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24937 AN: 152006 Hom.: 2183 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24959 AN: 152124 Hom.: 2188 Cov.: 32 AF XY: 0.164 AC XY: 12222 AN XY: 74376

African (AFR) AF: 0.144 AC: 5997 AN: 41516

American (AMR) AF: 0.129 AC: 1971 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.0567 AC: 294 AN: 5184

South Asian (SAS) AF: 0.0984 AC: 474 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2806 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12408 AN: 67980

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.156 Hom.: 1077

Bravo AF: 0.155

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs6861611; hg19: chr5-169563583;