rs2256842

Variant names:

• chr7-118764554-A-G
• rs2256842
• ENST00000761310.1:n.170T>C

Variant summary

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

The ENST00000761310.1(ENSG00000299159):​n.170T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,148 control chromosomes in the GnomAD database, including 2,569 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 0.11 (2569 hom., cov: 32)
• Consequence: ENSG00000299159 ENST00000761310.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 0 publications found

Genes affected

ENSG00000299159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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
ENSG00000299159	ENST00000761310.1	n.170T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000299176	ENST00000761416.1	n.125+553A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16047 AN: 152030 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0100

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00975

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.106 AC: 16089 AN: 152148 Hom.: 2569 Cov.: 32 AF XY: 0.102 AC XY: 7582 AN XY: 74398

African (AFR) AF: 0.346 AC: 14328 AN: 41442

American (AMR) AF: 0.0444 AC: 680 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4824

European-Finnish (FIN) AF: 0.0100 AC: 106 AN: 10604

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00973 AC: 662 AN: 68018

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0801 Hom.: 243

Bravo AF: 0.118

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2256842; hg19: chr7-118404608;