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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802609.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304344	ENST00000802609.1		n.68-967C>T		intron	N/A
	ENSG00000304344	ENST00000802610.1		n.135-967C>T		intron	N/A
	ENSG00000304344	ENST00000802611.1		n.139-967C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2770228;

hg19: chr13-98200572;