rs941796

Positions:

• chr20-41662167-G-A
• chr20-41662167-G-C

Variant summary

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

The ENST00000685138.2(ENSG00000288843):​n.273-38463C>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 0.519 in 152,042 control chromosomes in the GnomAD database, including 22,278 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 0.52 (22278 hom., cov: 32)
• Consequence: ENST00000685138.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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
	ENST00000685138.2	n.273-38463C>T		intron_variant, non_coding_transcript_variant
	ENST00000686898.1	n.238-11659C>T		intron_variant, non_coding_transcript_variant
	ENST00000691734.1	n.356-11659C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78789 AN: 151924 Hom.: 22231 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.519 AC: 78899 AN: 152042 Hom.: 22278 Cov.: 32 AF XY: 0.521 AC XY: 38759 AN XY: 74332

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.474

Alfa AF: 0.426 Hom.: 14573

Bravo AF: 0.529

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941796; hg19: chr20-40290806;