rs4793501

Variant names:

• chr17-70722593-C-T
• rs4793501
• ENST00000774266.1:n.156-59C>T

Variant summary

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

The ENST00000774266.1(ENSG00000300827):​n.156-59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,918 control chromosomes in the GnomAD database, including 31,522 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 0.64 (31522 hom., cov: 31)
• Consequence: ENSG00000300827 ENST00000774266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 16 publications found

Genes affected

ENSG00000300827 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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
ENSG00000300827	ENST00000774266.1	n.156-59C>T		intron_variant	Intron 1 of 3
ENSG00000300827	ENST00000774267.1	n.95-59C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96404 AN: 151800 Hom.: 31484 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.635 AC: 96493 AN: 151918 Hom.: 31522 Cov.: 31 AF XY: 0.630 AC XY: 46767 AN XY: 74248

African (AFR) AF: 0.785 AC: 32559 AN: 41488

American (AMR) AF: 0.624 AC: 9522 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2055 AN: 5138

South Asian (SAS) AF: 0.519 AC: 2494 AN: 4810

European-Finnish (FIN) AF: 0.521 AC: 5484 AN: 10526

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40225 AN: 67926

Other (OTH) AF: 0.657 AC: 1376 AN: 2094

Alfa AF: 0.609 Hom.: 90522

Bravo AF: 0.647

Asia WGS AF: 0.486 AC: 1691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.60
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4793501; hg19: chr17-68718734;