rs4140483

Variant names:

• chr6-100245132-G-A
• rs4140483

Your query was ambiguous. Multiple possible variants found:

• chr6-100245132-G-A
• chr6-100245132-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 0.153 in 152,074 control chromosomes in the GnomAD database, including 1,829 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 (1829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 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: 0.153 AC: 23265 AN: 151956 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23281 AN: 152074 Hom.: 1829 Cov.: 32 AF XY: 0.155 AC XY: 11540 AN XY: 74348

African (AFR) AF: 0.140 AC: 5809 AN: 41476

American (AMR) AF: 0.180 AC: 2754 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.128 AC: 661 AN: 5170

South Asian (SAS) AF: 0.186 AC: 897 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1752 AN: 10580

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10261 AN: 67974

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.157 Hom.: 3255

Bravo AF: 0.152

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.51
DANN	Benign	0.61
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs4140483; hg19: chr6-100693008; COSMIC: COSV68670537;