rs775448

Variant names:

• chr12-69723630-G-A
• rs775448
• ENST00000501387.7:n.592+1592C>T

Variant summary

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

The ENST00000501387.7(ENSG00000247131):​n.592+1592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,008 control chromosomes in the GnomAD database, including 8,193 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 0.32 (8193 hom., cov: 31)
• Consequence: ENSG00000247131 ENST00000501387.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 9 publications found

Genes affected

ENSG00000247131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928002	NR_110072.2	n.565+1592C>T		intron_variant	Intron 3 of 3
LOC101928002	NR_159971.1	n.442-1059C>T		intron_variant	Intron 2 of 2
LOC101928002	NR_159972.1	n.441+1592C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247131	ENST00000501387.7	n.592+1592C>T		intron_variant	Intron 3 of 3	1
ENSG00000247131	ENST00000501300.2	n.489-1059C>T		intron_variant	Intron 2 of 2	5
ENSG00000247131	ENST00000661191.2	n.514+1592C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48668 AN: 151890 Hom.: 8190 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152008 Hom.: 8193 Cov.: 31 AF XY: 0.323 AC XY: 23992 AN XY: 74298

African (AFR) AF: 0.228 AC: 9449 AN: 41472

American (AMR) AF: 0.300 AC: 4591 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1280 AN: 5170

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4824

European-Finnish (FIN) AF: 0.406 AC: 4282 AN: 10538

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25258 AN: 67940

Other (OTH) AF: 0.306 AC: 645 AN: 2106

Alfa AF: 0.345 Hom.: 7015

Bravo AF: 0.302

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.3
DANN	Benign	0.78
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs775448; hg19: chr12-70117410;