chr4-27962783-A-T

Variant names:

• chr4-27962783-A-T
• rs11934750
• ENST00000846268.1:n.185-30656A>T

Variant summary

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

The ENST00000846268.1(ENSG00000287389):​n.185-30656A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 150,802 control chromosomes in the GnomAD database, including 5,575 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 0.23 (5575 hom., cov: 31)
• Consequence: ENSG00000287389 ENST00000846268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 1 publications found

Genes affected

ENSG00000287389 (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 (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374552	XR_001741500.1	n.156-30706A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287389	ENST00000846268.1	n.185-30656A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 33954 AN: 150686 Hom.: 5559 Cov.: 31

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.226 AC: 34008 AN: 150802 Hom.: 5575 Cov.: 31 AF XY: 0.220 AC XY: 16225 AN XY: 73786

African (AFR) AF: 0.472 AC: 19160 AN: 40636

American (AMR) AF: 0.165 AC: 2504 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3466

East Asian (EAS) AF: 0.0175 AC: 90 AN: 5140

South Asian (SAS) AF: 0.127 AC: 612 AN: 4802

European-Finnish (FIN) AF: 0.109 AC: 1149 AN: 10526

Middle Eastern (MID) AF: 0.200 AC: 58 AN: 290

European-Non Finnish (NFE) AF: 0.138 AC: 9337 AN: 67746

Other (OTH) AF: 0.217 AC: 457 AN: 2108

Alfa AF: 0.0547 Hom.: 65

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.33
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11934750; hg19: chr4-27964405;