3-37193098-C-T

Variant summary

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

The ENST00000702636.1(ENSG00000290046):n.198-11577C>T variant causes a intron, non coding transcript 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: ENST00000702636.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377642	XR_007095869.1	n.111-11494C>T		intron_variant, non_coding_transcript_variant
LOC105377642	XR_002959625.2	n.208-11577C>T		intron_variant, non_coding_transcript_variant
LOC105377642	XR_007095870.1	n.208-11577C>T		intron_variant, non_coding_transcript_variant
LOC105377642	XR_007095871.1	n.111-11577C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702636.1	n.198-11577C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.435

Alfa AF: 0.463 Hom.: 27288

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7631605; hg19: chr3-37234589;