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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826985.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307544	ENST00000826985.1		n.210-2761A>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10893845;

hg19: chr11-128186882;