rs4646410

Positions:

• chr17-17505385-G-A
• chr17-17505385-G-C

Variant summary

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

The ENST00000671231.1(ENSG00000286430):​n.120+1261G>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 0.562 in 151,866 control chromosomes in the GnomAD database, including 26,765 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 0.56 (26765 hom., cov: 31)
• Consequence: ENST00000671231.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 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
	ENST00000671231.1	n.120+1261G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85277 AN: 151748 Hom.: 26761 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.562 AC: 85309 AN: 151866 Hom.: 26765 Cov.: 31 AF XY: 0.557 AC XY: 41334 AN XY: 74216

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.570

Alfa AF: 0.679 Hom.: 31798

Bravo AF: 0.540

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4646410; hg19: chr17-17408699;