rs4746077

Positions:

• chr10-71020361-T-A

Variant summary

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

The ENST00000646051.1(ENSG00000285300):​n.259-6218T>A 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 0.832 in 152,208 control chromosomes in the GnomAD database, including 52,887 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 0.83 (52887 hom., cov: 33)
• Consequence: ENST00000646051.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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 (NFE) allele frequency at 95% confidence interval = 0.859 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
	ENST00000646051.1	n.259-6218T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126520 AN: 152090 Hom.: 52843 Cov.: 33

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.832 AC: 126620 AN: 152208 Hom.: 52887 Cov.: 33 AF XY: 0.829 AC XY: 61678 AN XY: 74406

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.852

Alfa AF: 0.845 Hom.: 6742

Bravo AF: 0.824

Asia WGS AF: 0.775 AC: 2694 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	4.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4746077; hg19: chr10-72780118;