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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377642	XR_002959625.2	n.208-11577C>T		intron_variant	Intron 1 of 3
LOC105377642	XR_007095869.1	n.111-11494C>T		intron_variant	Intron 1 of 2
LOC105377642	XR_007095870.1	n.208-11577C>T		intron_variant	Intron 1 of 3
LOC105377642	XR_007095871.1	n.111-11577C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290046	ENST00000702636.1	n.198-11577C>T		intron_variant	Intron 1 of 3
ENSG00000290046	ENST00000737037.1	n.110-12730C>T		intron_variant	Intron 1 of 2
ENSG00000290046	ENST00000737038.1	n.108-11577C>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs7631605; hg19: chr3-37234589;