rs7561696

Variant names:

• chr2-48076712-A-G
• rs7561696
• ENST00000447571.5:n.241-73287T>C

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.241-73287T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,214 control chromosomes in the GnomAD database, including 1,459 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 (1459 hom., cov: 33)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 4 publications found

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907765	XR_007086314.1	n.404-13395A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230773	ENST00000447571.5	n.241-73287T>C		intron_variant	Intron 3 of 8	1
ENSG00000230773	ENST00000587616.1	n.190+32824T>C		intron_variant	Intron 2 of 10	5
ENSG00000230773	ENST00000649883.1	n.201+72263T>C		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19392 AN: 152098 Hom.: 1454 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.128 AC: 19417 AN: 152214 Hom.: 1459 Cov.: 33 AF XY: 0.125 AC XY: 9277 AN XY: 74432

African (AFR) AF: 0.176 AC: 7298 AN: 41488

American (AMR) AF: 0.0848 AC: 1297 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4830

European-Finnish (FIN) AF: 0.149 AC: 1585 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8658 AN: 68018

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.128 Hom.: 252

Bravo AF: 0.125

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.57
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs7561696; hg19: chr2-48303851;