rs496547

Positions:

• chr11-118705754-A-T

Variant summary

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

The ENST00000526274.2(ENSG00000255422):​n.231+916A>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 0.639 in 151,632 control chromosomes in the GnomAD database, including 31,168 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 0.64 (31168 hom., cov: 29)
• Consequence: ENST00000526274.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369519	XR_007062909.1	n.482+916A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000526274.2	n.231+916A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000646572.2	n.460+916A>T		intron_variant, non_coding_transcript_variant
	ENST00000702882.1	n.389+916A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96795 AN: 151518 Hom.: 31132 Cov.: 29

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.639 AC: 96882 AN: 151632 Hom.: 31168 Cov.: 29 AF XY: 0.637 AC XY: 47204 AN XY: 74052

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.659

Alfa AF: 0.639 Hom.: 3896

Bravo AF: 0.643

Asia WGS AF: 0.675 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs496547; hg19: chr11-118576463; COSMIC: COSV65996544;