rs10456051

chr6-27495657-T-C

Variant summary

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

The ENST00000648816.1(ENSG00000285703):n.218+331A>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 0.0488 in 152,330 control chromosomes in the GnomAD database, including 262 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 0.049 (262 hom., cov: 32)
• Consequence: ENST00000648816.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0713 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
	ENST00000648816.1	n.218+331A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7435 AN: 152212 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0488 AC: 7435 AN: 152330 Hom.: 262 Cov.: 32 AF XY: 0.0492 AC XY: 3662 AN XY: 74476

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0637 Hom.: 478

Bravo AF: 0.0431

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10456051; hg19: chr6-27463436;