rs7616661

Variant names:

• chr3-5923856-T-G
• rs7616661
• ENST00000425894.2:n.572-38869T>G

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.572-38869T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.065 in 152,188 control chromosomes in the GnomAD database, including 680 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 0.065 (680 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425894.2. 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
	ENSG00000229642	ENST00000425894.2	TSL:3	n.572-38869T>G		intron	N/A
	ENSG00000229642	ENST00000779001.1		n.718+17931T>G		intron	N/A
	ENSG00000229642	ENST00000779002.1		n.343-38869T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9863 AN: 152070 Hom.: 673 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0185

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0650 AC: 9895 AN: 152188 Hom.: 680 Cov.: 32 AF XY: 0.0660 AC XY: 4910 AN XY: 74410

African (AFR) AF: 0.142 AC: 5891 AN: 41488

American (AMR) AF: 0.0299 AC: 458 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0185 AC: 64 AN: 3466

East Asian (EAS) AF: 0.255 AC: 1316 AN: 5160

South Asian (SAS) AF: 0.110 AC: 529 AN: 4820

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10614

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0194 AC: 1322 AN: 68018

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0392 Hom.: 68

Bravo AF: 0.0685

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.49
PhyloP100		-0.64

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: rs7616661;

hg19: chr3-5965543;