6-72441923-C-T

Variant names:

• chr6-72441923-C-T
• rs10498883
• ENST00000728467.1:n.147-22341C>T

Variant summary

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

The ENST00000728467.1(ENSG00000295177):​n.147-22341C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,980 control chromosomes in the GnomAD database, including 3,562 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 0.21 (3562 hom., cov: 33)
• Consequence: ENSG00000295177 ENST00000728467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 publications found

Genes affected

ENSG00000295177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 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
ENSG00000295177	ENST00000728467.1	n.147-22341C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31784 AN: 151862 Hom.: 3557 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31810 AN: 151980 Hom.: 3562 Cov.: 33 AF XY: 0.208 AC XY: 15451 AN XY: 74282

African (AFR) AF: 0.272 AC: 11256 AN: 41440

American (AMR) AF: 0.293 AC: 4472 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5166

South Asian (SAS) AF: 0.134 AC: 643 AN: 4812

European-Finnish (FIN) AF: 0.155 AC: 1641 AN: 10560

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11326 AN: 67954

Other (OTH) AF: 0.206 AC: 435 AN: 2116

Alfa AF: 0.207 Hom.: 1556

Bravo AF: 0.228

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10498883; hg19: chr6-73151625;