rs2770228

Variant names:

• chr13-97548318-G-A
• rs2770228
• ENST00000802609.1:n.68-967C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-97548318-G-A
• chr13-97548318-G-C
• chr13-97548318-G-T

Variant summary

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

The ENST00000802609.1(ENSG00000304344):​n.68-967C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,202 control chromosomes in the GnomAD database, including 63,315 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 0.91 (63315 hom., cov: 31)
• Consequence: ENSG00000304344 ENST00000802609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 5 publications found

Genes affected

ENSG00000304344 (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 (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370325	XR_001749969.1	n.105-243G>A		intron_variant	Intron 1 of 2
LOC105370324	XR_007063845.1	n.2615-967C>T		intron_variant	Intron 3 of 5
LOC105370324	XR_931663.3	n.2671-967C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304344	ENST00000802609.1	n.68-967C>T		intron_variant	Intron 1 of 2
ENSG00000304344	ENST00000802610.1	n.135-967C>T		intron_variant	Intron 2 of 3
ENSG00000304344	ENST00000802611.1	n.139-967C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137790 AN: 152084 Hom.: 63280 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.939

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.906 AC: 137879 AN: 152202 Hom.: 63315 Cov.: 31 AF XY: 0.910 AC XY: 67711 AN XY: 74420

African (AFR) AF: 0.736 AC: 30522 AN: 41452

American (AMR) AF: 0.955 AC: 14609 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3365 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5179 AN: 5182

South Asian (SAS) AF: 0.966 AC: 4651 AN: 4816

European-Finnish (FIN) AF: 0.990 AC: 10513 AN: 10618

Middle Eastern (MID) AF: 0.942 AC: 275 AN: 292

European-Non Finnish (NFE) AF: 0.970 AC: 65996 AN: 68044

Other (OTH) AF: 0.919 AC: 1942 AN: 2114

Alfa AF: 0.931 Hom.: 20779

Bravo AF: 0.895

Asia WGS AF: 0.964 AC: 3351 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	1.1
DANN	Benign	0.29
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2770228; hg19: chr13-98200572;