rs7607015

Variant names:

• chr2-81586157-C-A
• rs7607015
• NR_187691.1:n.497+37410C>A

Variant summary

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

The NR_187691.1(LOC102724542):​n.497+37410C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,686 control chromosomes in the GnomAD database, including 4,854 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 0.18 (4854 hom., cov: 32)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 3 publications found

Genes affected

LOC102724542 (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 = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724542	NR_187691.1	n.497+37410C>A		intron_variant	Intron 2 of 3
LOC102724542	NR_187692.1	n.575+6548C>A		intron_variant	Intron 3 of 4
LOC102724542	NR_187693.1	n.497+37410C>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26740 AN: 151570 Hom.: 4825 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.177 AC: 26820 AN: 151686 Hom.: 4854 Cov.: 32 AF XY: 0.170 AC XY: 12636 AN XY: 74176

African (AFR) AF: 0.452 AC: 18546 AN: 41044

American (AMR) AF: 0.119 AC: 1813 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.0528 AC: 273 AN: 5172

South Asian (SAS) AF: 0.0365 AC: 176 AN: 4826

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10592

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4938 AN: 67998

Other (OTH) AF: 0.147 AC: 310 AN: 2110

Alfa AF: 0.111 Hom.: 2587

Bravo AF: 0.196

Asia WGS AF: 0.0780 AC: 272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.39
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs7607015; hg19: chr2-81813281;