rs7607490

Variant names:

• chr2-12710994-G-A
• rs7607490
• XR_007086222.1:n.5765C>T

Variant summary

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

The XR_007086222.1(LOC124905974):​n.5765C>T variant causes a non coding transcript exon 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: LOC124905974 XR_007086222.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 8 publications found

Genes affected

LOC124905974 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657078.2. 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
	ENSG00000286427	ENST00000657078.2		n.389+5370C>T		intron	N/A
	ENSG00000286427	ENST00000840615.1		n.282+5370C>T		intron	N/A

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

African (AFR) AF: 0.204 AC: 8446 AN: 41454

American (AMR) AF: 0.0884 AC: 1351 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.127 AC: 608 AN: 4806

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10604

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7314 AN: 67996

Other (OTH) AF: 0.118 AC: 250 AN: 2116

Alfa AF: 0.109 Hom.: 704

Bravo AF: 0.131

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.27
PhyloP100		-0.092

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: rs7607490;

hg19: chr2-12851120;