rs502943

Positions:

• chr11-56812140-T-A

Variant summary

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

The ENST00000627642.1(ENSG00000290749):​n.322+7961A>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 0.651 in 151,422 control chromosomes in the GnomAD database, including 32,266 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 0.65 (32266 hom., cov: 31)
• Consequence: ENST00000627642.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

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 (SAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000627642.1	n.322+7961A>T		intron_variant, non_coding_transcript_variant
	ENST00000378368.4	n.128+7441A>T		intron_variant, non_coding_transcript_variant
	ENST00000531887.1	n.67+7441A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98437 AN: 151304 Hom.: 32221 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.651 AC: 98544 AN: 151422 Hom.: 32266 Cov.: 31 AF XY: 0.659 AC XY: 48733 AN XY: 73970

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.641

Alfa AF: 0.623 Hom.: 3685

Bravo AF: 0.639

Asia WGS AF: 0.805 AC: 2800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs502943; hg19: chr11-56579616;