rs10065906

Positions:

• chr5-159580770-C-A
• chr5-159580770-C-G
• chr5-159580770-C-T

Variant summary

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

The ENST00000636819.1(ENSG00000249738):​n.44+27725C>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 0.733 in 152,104 control chromosomes in the GnomAD database, including 41,750 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 0.73 (41750 hom., cov: 32)
• Consequence: ENST00000636819.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377684	XR_941139.3	n.2229+335C>A		intron_variant, non_coding_transcript_variant
LOC105377684	XR_941141.2	n.570+335C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636819.1	n.44+27725C>A		intron_variant, non_coding_transcript_variant		5
	ENST00000642094.1	n.323+335C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111342 AN: 151986 Hom.: 41695 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.733 AC: 111457 AN: 152104 Hom.: 41750 Cov.: 32 AF XY: 0.725 AC XY: 53900 AN XY: 74328

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.742

Alfa AF: 0.688 Hom.: 56814

Bravo AF: 0.744

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10065906; hg19: chr5-159007778;