rs41504145

Positions:

• chr21-25227941-T-C

Variant summary

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

The ENST00000656005.1(ENSG00000222042):​n.218-52496A>G 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 0.129 in 151,528 control chromosomes in the GnomAD database, including 3,209 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 0.13 (3209 hom., cov: 31)
• Consequence: ENST00000656005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 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
	ENST00000656005.1	n.218-52496A>G		intron_variant, non_coding_transcript_variant
	ENST00000409758.1	n.90-52496A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000667825.1	n.190-52496A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19464 AN: 151410 Hom.: 3190 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00658

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0897

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

GnomAD4 genome AF: 0.129 AC: 19529 AN: 151528 Hom.: 3209 Cov.: 31 AF XY: 0.125 AC XY: 9272 AN XY: 74040

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.0559

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.00660

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0862 Hom.: 253

Bravo AF: 0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41504145; hg19: chr21-26600255;