rs4959270

Variant names:

• chr6-457748-C-A
• rs4959270
• ENST00000661640.1:n.335+4023C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661640.1(ENSG00000286364):​n.335+4023C>A variant causes a intron 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: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286364	ENST00000661640.1	n.335+4023C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.259 AC: 10745 AN: 41444

American (AMR) AF: 0.485 AC: 7411 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5168

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4814

European-Finnish (FIN) AF: 0.469 AC: 4961 AN: 10574

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33158 AN: 67942

Other (OTH) AF: 0.443 AC: 936 AN: 2114

Alfa AF: 0.448 Hom.: 31314

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
PhyloP100		0.21

Splicing

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

Publications

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Other links and lift over

dbSNP: rs4959270; hg19: chr6-457748;