rs11763972

Positions:

• chr7-26614773-G-A
• chr7-26614773-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661238.1(ENSG00000286507):​n.48+2475C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,898 control chromosomes in the GnomAD database, including 2,024 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 0.16 (2024 hom., cov: 32)
• Consequence: ENST00000661238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928077	XR_007060264.1	n.1166+2475C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661238.1	n.48+2475C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23732 AN: 151780 Hom.: 2018 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.156 AC: 23751 AN: 151898 Hom.: 2024 Cov.: 32 AF XY: 0.157 AC XY: 11630 AN XY: 74244

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.141

Alfa AF: 0.134 Hom.: 1743

Bravo AF: 0.156

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11763972; hg19: chr7-26654392;