11-104346753-T-C

Variant names:

• chr11-104346753-T-C
• rs10895656
• ENST00000835153.1:n.223+9866T>C

Variant summary

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

The ENST00000835153.1(ENSG00000308576):​n.223+9866T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,042 control chromosomes in the GnomAD database, including 14,971 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 0.44 (14971 hom., cov: 33)
• Consequence: ENSG00000308576 ENST00000835153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 publications found

Genes affected

ENSG00000308576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835153.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308576	ENST00000835153.1		n.223+9866T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67037 AN: 151924 Hom.: 14940 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.441 AC: 67119 AN: 152042 Hom.: 14971 Cov.: 33 AF XY: 0.440 AC XY: 32690 AN XY: 74292

African (AFR) AF: 0.459 AC: 19058 AN: 41494

American (AMR) AF: 0.415 AC: 6317 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1845 AN: 5170

South Asian (SAS) AF: 0.550 AC: 2647 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4377 AN: 10562

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30118 AN: 67992

Other (OTH) AF: 0.446 AC: 939 AN: 2104

Alfa AF: 0.437 Hom.: 24462

Bravo AF: 0.437

Asia WGS AF: 0.482 AC: 1676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10895656; hg19: chr11-104217481;