rs767210

Variant names:

• chr13-110817691-G-A
• rs767210
• ENST00000755406.1:n.440-1099G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-110817691-G-A
• chr13-110817691-G-C
• chr13-110817691-G-T

Variant summary

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

The ENST00000755406.1(ENSG00000298419):​n.440-1099G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,224 control chromosomes in the GnomAD database, including 1,025 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 0.10 (1025 hom., cov: 33)
• Consequence: ENSG00000298419 ENST00000755406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 7 publications found

Genes affected

ENSG00000298419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370362	NR_158538.1	n.70-1099G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298419	ENST00000755406.1	n.440-1099G>A		intron_variant	Intron 2 of 2
ENSG00000298419	ENST00000755407.1	n.482-1099G>A		intron_variant	Intron 3 of 3
ENSG00000298419	ENST00000755408.1	n.170-1099G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15285 AN: 152106 Hom.: 1030 Cov.: 33

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.100 AC: 15275 AN: 152224 Hom.: 1025 Cov.: 33 AF XY: 0.102 AC XY: 7592 AN XY: 74432

African (AFR) AF: 0.0232 AC: 962 AN: 41546

American (AMR) AF: 0.0963 AC: 1473 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3472

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5190

South Asian (SAS) AF: 0.191 AC: 923 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10586

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9245 AN: 67996

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.117 Hom.: 2939

Bravo AF: 0.0859

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs767210; hg19: chr13-111470038;