rs7963343

Variant names:

• chr12-93901846-T-G
• rs7963343
• ENST00000550687.1:n.140-6481A>C

Variant summary

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

The ENST00000550687.1(ENSG00000257283):​n.140-6481A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,184 control chromosomes in the GnomAD database, including 2,281 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 0.17 (2281 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000550687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 3 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550687.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369911	NR_135017.1		n.143-6481A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257283	ENST00000550687.1	TSL:4	n.140-6481A>C		intron	N/A
	ENSG00000257283	ENST00000786429.1		n.277-6481A>C		intron	N/A
	ENSG00000257283	ENST00000786431.1		n.165-6481A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25580 AN: 152066 Hom.: 2273 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.168 AC: 25608 AN: 152184 Hom.: 2281 Cov.: 32 AF XY: 0.169 AC XY: 12550 AN XY: 74426

African (AFR) AF: 0.172 AC: 7137 AN: 41496

American (AMR) AF: 0.195 AC: 2977 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3470

East Asian (EAS) AF: 0.0391 AC: 203 AN: 5186

South Asian (SAS) AF: 0.114 AC: 549 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2199 AN: 10590

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

European-Non Finnish (NFE) AF: 0.171 AC: 11639 AN: 68012

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.169 Hom.: 1515

Bravo AF: 0.170

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7963343; hg19: chr12-94295622;