rs4959270

Positions:

• chr6-457748-C-A
• chr6-457748-C-G
• chr6-457748-C-T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.335+4023C>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 0.41 in 152,016 control chromosomes in the GnomAD database, including 13,643 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 0.41 (13643 hom., cov: 32)
• Consequence: ENST00000661640.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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
	ENST00000661640.1	n.335+4023C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62294 AN: 151896 Hom.: 13632 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.410 AC: 62336 AN: 152016 Hom.: 13643 Cov.: 32 AF XY: 0.407 AC XY: 30243 AN XY: 74324

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.443

Alfa AF: 0.464 Hom.: 22579

Bravo AF: 0.406

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959270; hg19: chr6-457748;