rs3120139

Variant names:

• chr6-160320590-G-A
• rs3120139

Your query was ambiguous. Multiple possible variants found:

• chr6-160320590-G-A
• chr6-160320590-G-C
• chr6-160320590-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 0.157 in 152,160 control chromosomes in the GnomAD database, including 2,138 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 (2138 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.157 AC: 23894 AN: 152042 Hom.: 2138 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.157 AC: 23905 AN: 152160 Hom.: 2138 Cov.: 33 AF XY: 0.151 AC XY: 11221 AN XY: 74402

African (AFR) AF: 0.237 AC: 9824 AN: 41496

American (AMR) AF: 0.0952 AC: 1456 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.152 AC: 788 AN: 5176

South Asian (SAS) AF: 0.0662 AC: 319 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10598

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9760 AN: 67994

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.141 Hom.: 5089

Bravo AF: 0.157

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.31
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs3120139; hg19: chr6-160741622; COSMIC: COSV69432067;