ENST00000702722.2:n.276-1035T>C

Variant names:

• chr1-94552963-T-C
• rs841698
• ENST00000702722.2:n.276-1035T>C

Variant summary

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

The ENST00000702722.2(ENSG00000288736):​n.276-1035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,234 control chromosomes in the GnomAD database, including 65,746 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 0.92 (65746 hom., cov: 32)
• Consequence: ENSG00000288736 ENST00000702722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.93
• Publications: 4 publications found

Genes affected

ENSG00000288736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702722.2. 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
	ENSG00000288736	ENST00000702722.2		n.276-1035T>C		intron	N/A
	ENSG00000288736	ENST00000837291.1		n.416-1035T>C		intron	N/A
	ENSG00000288736	ENST00000837292.1		n.1037-1035T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140515 AN: 152116 Hom.: 65735 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.987

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.933

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

GnomAD4 genome AF: 0.923 AC: 140576 AN: 152234 Hom.: 65746 Cov.: 32 AF XY: 0.925 AC XY: 68881 AN XY: 74430

African (AFR) AF: 0.754 AC: 31302 AN: 41492

American (AMR) AF: 0.933 AC: 14278 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3461 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5106 AN: 5166

South Asian (SAS) AF: 0.987 AC: 4760 AN: 4822

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10620

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67889 AN: 68046

Other (OTH) AF: 0.930 AC: 1967 AN: 2114

Alfa AF: 0.962 Hom.: 119929

Bravo AF: 0.910

Asia WGS AF: 0.965 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs841698; hg19: chr1-95018519;