3-37193098-C-T

Variant names:

• chr3-37193098-C-T
• rs7631605
• ENST00000702636.1:n.198-11577C>T

Variant summary

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

The ENST00000702636.1(ENSG00000290046):​n.198-11577C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 150,200 control chromosomes in the GnomAD database, including 15,676 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 0.45 (15676 hom., cov: 28)
• Consequence: ENSG00000290046 ENST00000702636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 24 publications found

Genes affected

ENSG00000290046 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702636.1. 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
	ENSG00000290046	ENST00000702636.1		n.198-11577C>T		intron	N/A
	ENSG00000290046	ENST00000737037.1		n.110-12730C>T		intron	N/A
	ENSG00000290046	ENST00000737038.1		n.108-11577C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67065 AN: 150108 Hom.: 15665 Cov.: 28

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.447 AC: 67107 AN: 150200 Hom.: 15676 Cov.: 28 AF XY: 0.438 AC XY: 32070 AN XY: 73166

African (AFR) AF: 0.457 AC: 18609 AN: 40714

American (AMR) AF: 0.450 AC: 6754 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1486 AN: 3454

East Asian (EAS) AF: 0.0787 AC: 405 AN: 5148

South Asian (SAS) AF: 0.250 AC: 1197 AN: 4790

European-Finnish (FIN) AF: 0.402 AC: 4007 AN: 9968

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33108 AN: 67840

Other (OTH) AF: 0.435 AC: 904 AN: 2080

Alfa AF: 0.463 Hom.: 44359

Bravo AF: 0.450

Asia WGS AF: 0.213 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.17
PhyloP100		-0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7631605;

hg19: chr3-37234589;