rs224135

Positions:

• chr10-62707042-A-G

Variant summary

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

The ENST00000649548.1(ENSG00000238280):​n.160-20963T>C 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 0.679 in 152,062 control chromosomes in the GnomAD database, including 37,018 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 0.68 (37018 hom., cov: 32)
• Consequence: ENST00000649548.1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649548.1	n.160-20963T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103128 AN: 151944 Hom.: 36949 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.679 AC: 103258 AN: 152062 Hom.: 37018 Cov.: 32 AF XY: 0.675 AC XY: 50178 AN XY: 74308

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.647

Alfa AF: 0.616 Hom.: 19467

Bravo AF: 0.685

Asia WGS AF: 0.640 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224135; hg19: chr10-64466802;