1-73886165-C-T

Variant names:

• chr1-73886165-C-T
• rs6701710
• ENST00000649962.1:n.271+19764G>A

Variant summary

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

The ENST00000649962.1(ENSG00000285778):​n.271+19764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,020 control chromosomes in the GnomAD database, including 1,313 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 0.13 (1313 hom., cov: 32)
• Consequence: ENSG00000285778 ENST00000649962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33

Genes affected

ENSG00000285778 (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 (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285778	ENST00000649962.1	n.271+19764G>A		intron_variant	Intron 2 of 3
ENSG00000285778	ENST00000667324.1	n.148+28964G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19649 AN: 151904 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.129 AC: 19654 AN: 152020 Hom.: 1313 Cov.: 32 AF XY: 0.129 AC XY: 9576 AN XY: 74310

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.123

Alfa AF: 0.115 Hom.: 571

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6701710; hg19: chr1-74351848;