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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447571.5. 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
	ENSG00000230773	ENST00000447571.5	TSL:1	n.241-73287T>C		intron	N/A
	ENSG00000230773	ENST00000587616.1	TSL:5	n.190+32824T>C		intron	N/A
	ENSG00000230773	ENST00000649883.1		n.201+72263T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7561696;

hg19: chr2-48303851;