1-73886165-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000285778 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285778	ENST00000649962.1		n.271+19764G>A		intron	N/A
	ENSG00000285778	ENST00000667324.1		n.148+28964G>A		intron	N/A

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

African (AFR) AF: 0.148 AC: 6120 AN: 41454

American (AMR) AF: 0.0994 AC: 1517 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0871 AC: 302 AN: 3468

East Asian (EAS) AF: 0.107 AC: 554 AN: 5176

South Asian (SAS) AF: 0.196 AC: 943 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1166 AN: 10574

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8564 AN: 67958

Other (OTH) AF: 0.123 AC: 259 AN: 2106

Alfa AF: 0.116 Hom.: 661

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.40
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs6701710; hg19: chr1-74351848;