rs2350753

Variant names:

• chr6-73238417-C-T
• rs2350753
• ENST00000423730.3:n.295+3638G>A

Variant summary

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

The ENST00000423730.3(ENSG00000243501):​n.295+3638G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,108 control chromosomes in the GnomAD database, including 1,526 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 0.12 (1526 hom., cov: 33)
• Consequence: ENSG00000243501 ENST00000423730.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 6 publications found

Genes affected

ENSG00000243501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423730.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC122539213	NR_173145.1		n.960-2268G>A		intron	N/A
	LOC122539213	NR_173146.1		n.959+3638G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243501	ENST00000423730.3	TSL:5	n.295+3638G>A		intron	N/A	ENSP00000457270.2	F5H697

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18329 AN: 151990 Hom.: 1524 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.121 AC: 18349 AN: 152108 Hom.: 1526 Cov.: 33 AF XY: 0.120 AC XY: 8898 AN XY: 74354

African (AFR) AF: 0.222 AC: 9212 AN: 41472

American (AMR) AF: 0.133 AC: 2035 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1107 AN: 5182

South Asian (SAS) AF: 0.0559 AC: 269 AN: 4816

European-Finnish (FIN) AF: 0.0359 AC: 380 AN: 10576

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4680 AN: 67998

Other (OTH) AF: 0.126 AC: 266 AN: 2116

Alfa AF: 0.0821 Hom.: 889

Bravo AF: 0.135

Asia WGS AF: 0.149 AC: 519 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.26
PhyloP100		-0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2350753; hg19: chr6-73948140;