6-149418239-G-A

Variant names:

• chr6-149418239-G-A
• rs236999

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 0.129 in 152,128 control chromosomes in the GnomAD database, including 1,330 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 0.13 (1330 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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: 0.129 AC: 19534 AN: 152010 Hom.: 1321 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.129 AC: 19565 AN: 152128 Hom.: 1330 Cov.: 33 AF XY: 0.129 AC XY: 9572 AN XY: 74356

African (AFR) AF: 0.175 AC: 7276 AN: 41492

American (AMR) AF: 0.112 AC: 1714 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.113 AC: 588 AN: 5182

South Asian (SAS) AF: 0.0870 AC: 419 AN: 4816

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10560

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7621 AN: 67992

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Alfa AF: 0.133 Hom.: 542

Bravo AF: 0.128

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs236999; hg19: chr6-149739375;