6-18072260-G-A

Variant names:

• chr6-18072260-G-A
• rs4380755

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 0.151 in 152,010 control chromosomes in the GnomAD database, including 1,909 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 0.15 (1909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22880 AN: 151892 Hom.: 1908 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.151 AC: 22882 AN: 152010 Hom.: 1909 Cov.: 32 AF XY: 0.155 AC XY: 11524 AN XY: 74300

African (AFR) AF: 0.107 AC: 4441 AN: 41458

American (AMR) AF: 0.251 AC: 3831 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3464

East Asian (EAS) AF: 0.154 AC: 796 AN: 5184

South Asian (SAS) AF: 0.171 AC: 823 AN: 4818

European-Finnish (FIN) AF: 0.174 AC: 1831 AN: 10528

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10108 AN: 67998

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.161 Hom.: 880

Bravo AF: 0.153

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.015
DANN	Benign	0.66
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4380755; hg19: chr6-18072491;