rs571312

Variant names:

• chr18-60172536-C-A
• rs571312
• ENST00000764630.1:n.799-1799G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-60172536-C-A
• chr18-60172536-C-G
• chr18-60172536-C-T

Variant summary

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

The ENST00000764630.1(ENSG00000299555):​n.799-1799G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,014 control chromosomes in the GnomAD database, including 5,334 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 0.26 (5334 hom., cov: 33)
• Consequence: ENSG00000299555 ENST00000764630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 186 publications found

Genes affected

ENSG00000299555 (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 (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299555	ENST00000764630.1	n.799-1799G>T		intron_variant	Intron 1 of 2
ENSG00000299555	ENST00000764631.1	n.934+600G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38736 AN: 151896 Hom.: 5321 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.255 AC: 38786 AN: 152014 Hom.: 5334 Cov.: 33 AF XY: 0.252 AC XY: 18696 AN XY: 74324

African (AFR) AF: 0.343 AC: 14219 AN: 41442

American (AMR) AF: 0.165 AC: 2526 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3468

East Asian (EAS) AF: 0.181 AC: 937 AN: 5180

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1805 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15977 AN: 67958

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.238 Hom.: 19688

Bravo AF: 0.257

Asia WGS AF: 0.232 AC: 807 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	0.14
DANN	Benign	0.48
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs571312; hg19: chr18-57839769;