rs10495408

Positions:

• chr1-238400697-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665394.1(ENSG00000234464):​n.326-3784G>C variant causes a intron, non coding transcript 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: ENST00000665394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105373220	XR_949308.3	n.265-24741G>C		intron_variant, non_coding_transcript_variant
LOC105373220	XR_949311.3	n.191-24726G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665394.1	n.326-3784G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0210

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.00632

Gnomad4 NFE AF: 0.00641

Gnomad4 OTH AF: 0.0431

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495408; hg19: chr1-238563997;