11-128316987-T-G

Variant names:

• chr11-128316987-T-G
• rs10893845
• ENST00000826985.1:n.210-2761A>C

Variant summary

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

The ENST00000826985.1(ENSG00000307544):​n.210-2761A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,128 control chromosomes in the GnomAD database, including 11,943 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 0.37 (11943 hom., cov: 32)
• Consequence: ENSG00000307544 ENST00000826985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 14 publications found

Genes affected

ENSG00000307544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902787	XR_007062946.1	n.209-12512A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307544	ENST00000826985.1	n.210-2761A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55561 AN: 152010 Hom.: 11940 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.365 AC: 55563 AN: 152128 Hom.: 11943 Cov.: 32 AF XY: 0.360 AC XY: 26745 AN XY: 74346

African (AFR) AF: 0.128 AC: 5294 AN: 41518

American (AMR) AF: 0.402 AC: 6145 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1396 AN: 5184

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4816

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10560

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33444 AN: 67980

Other (OTH) AF: 0.404 AC: 855 AN: 2116

Alfa AF: 0.455 Hom.: 71670

Bravo AF: 0.358

Asia WGS AF: 0.325 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.32
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10893845; hg19: chr11-128186882;