rs10495408

Variant names:

• chr1-238400697-G-C
• rs10495408
• ENST00000665394.1:n.326-3784G>C

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.326-3784G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,206 control chromosomes in the GnomAD database, including 565 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 0.052 (565 hom., cov: 33)
• Consequence: ENSG00000234464 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 0 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373220	XR_949308.3	n.265-24741G>C		intron_variant	Intron 3 of 4
LOC105373220	XR_949311.3	n.191-24726G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234464	ENST00000665394.1	n.326-3784G>C		intron_variant	Intron 4 of 4
ENSG00000234464	ENST00000716116.1	n.131-24741G>C		intron_variant	Intron 1 of 4
ENSG00000234464	ENST00000716147.1	n.500+74423G>C		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7816 AN: 152088 Hom.: 558 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.00632

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00641

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0515 AC: 7845 AN: 152206 Hom.: 565 Cov.: 33 AF XY: 0.0502 AC XY: 3737 AN XY: 74436

African (AFR) AF: 0.162 AC: 6721 AN: 41500

American (AMR) AF: 0.0210 AC: 321 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3470

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5184

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4824

European-Finnish (FIN) AF: 0.00632 AC: 67 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00641 AC: 436 AN: 68012

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0290 Hom.: 29

Bravo AF: 0.0572

Asia WGS AF: 0.0310 AC: 109 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	0.40
DANN	Benign	0.32
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10495408; hg19: chr1-238563997;