chr6-127387102-T-C

Variant names:

• chr6-127387102-T-C
• rs11759744
• ENST00000761942.1:n.150+26023T>C

Variant summary

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

The ENST00000761942.1(ENSG00000299250):​n.150+26023T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 143,260 control chromosomes in the GnomAD database, including 8,383 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 0.31 (8383 hom., cov: 25)
• Consequence: ENSG00000299250 ENST00000761942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 4 publications found

Genes affected

ENSG00000299250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 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
ENSG00000299250	ENST00000761942.1	n.150+26023T>C		intron_variant	Intron 2 of 3
ENSG00000299250	ENST00000761943.1	n.224+26023T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 44564 AN: 143192 Hom.: 8382 Cov.: 25

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.00356

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.311 AC: 44561 AN: 143260 Hom.: 8383 Cov.: 25 AF XY: 0.301 AC XY: 20800 AN XY: 69034

African (AFR) AF: 0.120 AC: 4532 AN: 37736

American (AMR) AF: 0.282 AC: 3895 AN: 13834

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1502 AN: 3442

East Asian (EAS) AF: 0.00357 AC: 17 AN: 4762

South Asian (SAS) AF: 0.236 AC: 1081 AN: 4580

European-Finnish (FIN) AF: 0.346 AC: 3036 AN: 8768

Middle Eastern (MID) AF: 0.473 AC: 121 AN: 256

European-Non Finnish (NFE) AF: 0.437 AC: 29304 AN: 66990

Other (OTH) AF: 0.347 AC: 691 AN: 1992

Alfa AF: 0.392 Hom.: 14541

Bravo AF: 0.288

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.4
DANN	Benign	0.90
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs11759744; hg19: chr6-127708247;