rs4344422

Positions:

• chr10-111838426-T-C

Variant summary

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

The ENST00000656217.1(ENSG00000287231):​n.133-49322A>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 0.247 in 152,248 control chromosomes in the GnomAD database, including 5,609 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 0.25 (5609 hom., cov: 33)
• Consequence: ENST00000656217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 (NFE) allele frequency at 95% confidence interval = 0.342 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
	ENST00000656217.1	n.133-49322A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37551 AN: 152130 Hom.: 5603 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.247 AC: 37559 AN: 152248 Hom.: 5609 Cov.: 33 AF XY: 0.242 AC XY: 17995 AN XY: 74428

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.242

Alfa AF: 0.293 Hom.: 1693

Bravo AF: 0.236

Asia WGS AF: 0.137 AC: 478 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	2.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4344422; hg19: chr10-113598184;