rs2794256

Variant names:

• chr6-119622238-G-A
• rs2794256
• ENST00000701940.2:n.325-66787G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-119622238-G-A
• chr6-119622238-G-C
• chr6-119622238-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701940.2(ENSG00000287100):​n.325-66787G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,012 control chromosomes in the GnomAD database, including 5,485 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 0.26 (5485 hom., cov: 32)
• Consequence: ENSG00000287100 ENST00000701940.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 7 publications found

Genes affected

ENSG00000287100 (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 (SAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377975	NR_134600.1	n.252+71843G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287100	ENST00000701940.2	n.325-66787G>A		intron_variant	Intron 3 of 3
ENSG00000287100	ENST00000777516.1	n.318+71843G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39905 AN: 151894 Hom.: 5490 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 39923 AN: 152012 Hom.: 5485 Cov.: 32 AF XY: 0.267 AC XY: 19830 AN XY: 74328

African (AFR) AF: 0.219 AC: 9089 AN: 41466

American (AMR) AF: 0.291 AC: 4447 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3468

East Asian (EAS) AF: 0.133 AC: 690 AN: 5182

South Asian (SAS) AF: 0.377 AC: 1816 AN: 4814

European-Finnish (FIN) AF: 0.356 AC: 3756 AN: 10550

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18444 AN: 67954

Other (OTH) AF: 0.256 AC: 539 AN: 2102

Alfa AF: 0.264 Hom.: 3931

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs2794256; hg19: chr6-119943401;