rs7607490

Positions:

• chr2-12710994-G-A

Variant summary

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

The ENST00000657078.1(ENSG00000286427):​n.194+5370C>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 0.125 in 152,120 control chromosomes in the GnomAD database, including 1,431 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 (1431 hom., cov: 32)
• Consequence: ENST00000657078.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905974	XR_007086221.1	n.544+5221C>T		intron_variant, non_coding_transcript_variant
LOC124905974	XR_007086222.1	n.5765C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657078.1	n.194+5370C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19006 AN: 152002 Hom.: 1433 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.125 AC: 19015 AN: 152120 Hom.: 1431 Cov.: 32 AF XY: 0.120 AC XY: 8922 AN XY: 74372

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0375

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.118

Alfa AF: 0.115 Hom.: 583

Bravo AF: 0.131

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7607490; hg19: chr2-12851120;