11-123198534-A-T

Variant names:

• chr11-123198534-A-T
• rs1944607
• ENST00000531681.2:n.305+5442A>T

Variant summary

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

The ENST00000531681.2(ENSG00000254710):​n.305+5442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,068 control chromosomes in the GnomAD database, including 19,184 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 0.47 (19184 hom., cov: 32)
• Consequence: ENSG00000254710 ENST00000531681.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 2 publications found

Genes affected

ENSG00000254710 (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 (SAS) allele frequency at 95% confidence interval = 0.611 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
ENSG00000254710	ENST00000531681.2	n.305+5442A>T		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71214 AN: 151950 Hom.: 19175 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.468 AC: 71242 AN: 152068 Hom.: 19184 Cov.: 32 AF XY: 0.478 AC XY: 35524 AN XY: 74326

African (AFR) AF: 0.188 AC: 7783 AN: 41508

American (AMR) AF: 0.609 AC: 9304 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1816 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3072 AN: 5168

South Asian (SAS) AF: 0.629 AC: 3027 AN: 4810

European-Finnish (FIN) AF: 0.622 AC: 6570 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37936 AN: 67954

Other (OTH) AF: 0.495 AC: 1040 AN: 2100

Alfa AF: 0.351 Hom.: 1004

Bravo AF: 0.452

Asia WGS AF: 0.551 AC: 1915 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	0.39
DANN	Benign	0.42
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1944607; hg19: chr11-123069242;