rs4917766

Positions:

• chr10-97337434-G-A
• chr10-97337434-G-C

Variant summary

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

The ENST00000445808.4(ENSG00000225850):​n.408+2463G>A 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 0.503 in 151,848 control chromosomes in the GnomAD database, including 21,028 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 0.50 (21028 hom., cov: 30)
• Consequence: ENST00000445808.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378448	XR_007062258.1	n.126+2463G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000445808.4	n.408+2463G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76342 AN: 151736 Hom.: 21036 Cov.: 30

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.503 AC: 76343 AN: 151848 Hom.: 21028 Cov.: 30 AF XY: 0.508 AC XY: 37676 AN XY: 74188

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.560

Alfa AF: 0.583 Hom.: 33162

Bravo AF: 0.494

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917766; hg19: chr10-99097191;