chr6-127633469-A-C

Variant names:

• chr6-127633469-A-C
• rs2922249

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 0.448 in 151,790 control chromosomes in the GnomAD database, including 16,202 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 0.45 (16202 hom., cov: 31)
• Consequence: LOC100420743 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 7 publications found

Genes affected

LOC100420743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420743		n.127633469A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000219284	ENST00000403830.2	n.252-411T>G		intron_variant	Intron 2 of 2	6
ENSG00000305799	ENST00000813004.1	n.319+1152A>C		intron_variant	Intron 3 of 3
ENSG00000305799	ENST00000813005.1	n.191+10084A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67950 AN: 151672 Hom.: 16197 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.448 AC: 67960 AN: 151790 Hom.: 16202 Cov.: 31 AF XY: 0.440 AC XY: 32589 AN XY: 74148

African (AFR) AF: 0.367 AC: 15204 AN: 41410

American (AMR) AF: 0.339 AC: 5171 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3466

East Asian (EAS) AF: 0.137 AC: 704 AN: 5150

South Asian (SAS) AF: 0.378 AC: 1824 AN: 4822

European-Finnish (FIN) AF: 0.496 AC: 5227 AN: 10530

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36441 AN: 67852

Other (OTH) AF: 0.439 AC: 928 AN: 2114

Alfa AF: 0.492 Hom.: 27317

Bravo AF: 0.426

Asia WGS AF: 0.255 AC: 887 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.73
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs2922249; hg19: chr6-127954614;