rs10493509

Positions:

• chr1-72744134-G-A
• chr1-72744134-G-T

Variant summary

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

The ENST00000668734.1(ENSG00000225087):​n.415+5032C>T 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 0.0841 in 151,822 control chromosomes in the GnomAD database, including 1,580 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 0.084 (1580 hom., cov: 32)
• Consequence: ENST00000668734.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378798	XR_947515.3	n.377+5032C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668734.1	n.415+5032C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12736 AN: 151704 Hom.: 1579 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.00575

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00874

Gnomad OTH AF: 0.0625

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

GnomAD4 genome AF: 0.0841 AC: 12767 AN: 151822 Hom.: 1580 Cov.: 32 AF XY: 0.0810 AC XY: 6008 AN XY: 74214

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.00408

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.00575

Gnomad4 NFE AF: 0.00874

Gnomad4 OTH AF: 0.0618

Alfa AF: 0.0150 Hom.: 27

Bravo AF: 0.0954

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493509; hg19: chr1-73209817;