4-144616698-T-C

Variant names:

• chr4-144616698-T-C
• rs11947381
• ENST00000649263.1:n.328-200720A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-200720A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,010 control chromosomes in the GnomAD database, including 32,261 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 0.64 (32261 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 10 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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
ENSG00000285713	ENST00000649263.1	n.328-200720A>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+138459A>G		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97313 AN: 151892 Hom.: 32215 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.641 AC: 97421 AN: 152010 Hom.: 32261 Cov.: 32 AF XY: 0.651 AC XY: 48364 AN XY: 74298

African (AFR) AF: 0.785 AC: 32566 AN: 41464

American (AMR) AF: 0.665 AC: 10136 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4247 AN: 5166

South Asian (SAS) AF: 0.796 AC: 3839 AN: 4822

European-Finnish (FIN) AF: 0.641 AC: 6764 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36005 AN: 67968

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.586 Hom.: 19702

Bravo AF: 0.645

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11947381; hg19: chr4-145537850;