rs1923476

Variant names:

• chr6-39970647-C-T
• rs1923476
• ENST00000649703.2:n.211-9445C>T

Variant summary

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

The ENST00000649703.2(ENSG00000293066):​n.211-9445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 152,072 control chromosomes in the GnomAD database, including 541 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 0.061 (541 hom., cov: 32)
• Consequence: ENSG00000293066 ENST00000649703.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

ENSG00000293066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723789	XR_001744112.1	n.260-4073C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293066	ENST00000649703.2	n.211-9445C>T		intron_variant	Intron 3 of 4
ENSG00000293066	ENST00000741538.1	n.257-9445C>T		intron_variant	Intron 3 of 5
ENSG00000293066	ENST00000741539.1	n.153+7088C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0612 AC: 9300 AN: 151956 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.00576

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0612 AC: 9314 AN: 152072 Hom.: 541 Cov.: 32 AF XY: 0.0609 AC XY: 4526 AN XY: 74356

African (AFR) AF: 0.138 AC: 5737 AN: 41446

American (AMR) AF: 0.0760 AC: 1160 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3466

East Asian (EAS) AF: 0.127 AC: 655 AN: 5158

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4816

European-Finnish (FIN) AF: 0.00576 AC: 61 AN: 10594

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0191 AC: 1297 AN: 68008

Other (OTH) AF: 0.0706 AC: 149 AN: 2110

Alfa AF: 0.0401 Hom.: 91

Bravo AF: 0.0701

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1923476; hg19: chr6-39938386;