rs10495505

Variant names:

• chr2-4553972-C-T
• rs10495505
• ENST00000707165.1:n.621+43813C>T

Variant summary

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

The ENST00000707165.1(ENSG00000291325):​n.621+43813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 150,650 control chromosomes in the GnomAD database, including 5,772 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 0.28 (5772 hom., cov: 28)
• Consequence: ENSG00000291325 ENST00000707165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 5 publications found

Genes affected

ENSG00000291325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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
ENSG00000291325	ENST00000707165.1	n.621+43813C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41491 AN: 150536 Hom.: 5773 Cov.: 28

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.276 AC: 41517 AN: 150650 Hom.: 5772 Cov.: 28 AF XY: 0.277 AC XY: 20364 AN XY: 73492

African (AFR) AF: 0.304 AC: 12453 AN: 40942

American (AMR) AF: 0.202 AC: 3076 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1064 AN: 3460

East Asian (EAS) AF: 0.256 AC: 1311 AN: 5124

South Asian (SAS) AF: 0.362 AC: 1728 AN: 4772

European-Finnish (FIN) AF: 0.312 AC: 3168 AN: 10140

Middle Eastern (MID) AF: 0.214 AC: 62 AN: 290

European-Non Finnish (NFE) AF: 0.264 AC: 17880 AN: 67728

Other (OTH) AF: 0.267 AC: 556 AN: 2086

Alfa AF: 0.268 Hom.: 3164

Bravo AF: 0.266

Asia WGS AF: 0.315 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.12
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10495505; hg19: chr2-4601562;