8-53642640-A-C

Variant names:

• chr8-53642640-A-C
• rs11773966
• ENST00000811243.1:n.216+14910T>G

Variant summary

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

The ENST00000811243.1(ENSG00000305478):​n.216+14910T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.989 in 152,340 control chromosomes in the GnomAD database, including 74,526 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 0.99 (74526 hom., cov: 33)
• Consequence: ENSG00000305478 ENST00000811243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 6 publications found

Genes affected

ENSG00000305478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 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
ENSG00000305478	ENST00000811243.1	n.216+14910T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.989 AC: 150563 AN: 152222 Hom.: 74469 Cov.: 33

Gnomad AFR AF: 0.997

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.985

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.989 AC: 150679 AN: 152340 Hom.: 74526 Cov.: 33 AF XY: 0.989 AC XY: 73647 AN XY: 74480

African (AFR) AF: 0.997 AC: 41459 AN: 41580

American (AMR) AF: 0.985 AC: 15085 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3431 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5168 AN: 5168

South Asian (SAS) AF: 0.996 AC: 4812 AN: 4830

European-Finnish (FIN) AF: 0.987 AC: 10487 AN: 10620

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66947 AN: 68040

Other (OTH) AF: 0.987 AC: 2086 AN: 2114

Alfa AF: 0.992 Hom.: 16101

Bravo AF: 0.990

Asia WGS AF: 0.997 AC: 3468 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	0.69
DANN	Benign	0.35
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11773966; hg19: chr8-54555200;