chr11-44356606-C-T

Variant names:

• chr11-44356606-C-T
• rs11037965
• ENST00000830683.1:n.136+17175C>T

Variant summary

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

The ENST00000830683.1(ENSG00000308049):​n.136+17175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,226 control chromosomes in the GnomAD database, including 1,296 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 0.099 (1296 hom., cov: 32)
• Consequence: ENSG00000308049 ENST00000830683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 4 publications found

Genes affected

ENSG00000308049 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830683.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308049	ENST00000830683.1		n.136+17175C>T		intron	N/A
	ENSG00000308049	ENST00000830684.1		n.118-1050C>T		intron	N/A
	ENSG00000308066	ENST00000830812.1		n.196+2579G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0988 AC: 15034 AN: 152108 Hom.: 1282 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.0805

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0991 AC: 15083 AN: 152226 Hom.: 1296 Cov.: 32 AF XY: 0.0994 AC XY: 7398 AN XY: 74456

African (AFR) AF: 0.191 AC: 7917 AN: 41502

American (AMR) AF: 0.229 AC: 3507 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0426 AC: 148 AN: 3472

East Asian (EAS) AF: 0.0801 AC: 414 AN: 5170

South Asian (SAS) AF: 0.0920 AC: 444 AN: 4824

European-Finnish (FIN) AF: 0.00725 AC: 77 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2315 AN: 68026

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0758 Hom.: 490

Bravo AF: 0.118

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.83
DANN	Benign	0.71
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11037965; hg19: chr11-44378156;