rs1993894

Variant names:

• chr7-64357110-G-A
• rs1993894
• ENST00000752301.1:n.80+14023C>T

Variant summary

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

The ENST00000752301.1(ENSG00000287699):​n.80+14023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,678 control chromosomes in the GnomAD database, including 9,273 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 0.34 (9273 hom., cov: 30)
• Consequence: ENSG00000287699 ENST00000752301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 0 publications found

Genes affected

ENSG00000287699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 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
ENSG00000287699	ENST00000752301.1	n.80+14023C>T		intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1	n.50+14023C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51284 AN: 151560 Hom.: 9260 Cov.: 30

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.339 AC: 51347 AN: 151678 Hom.: 9273 Cov.: 30 AF XY: 0.336 AC XY: 24903 AN XY: 74126

African (AFR) AF: 0.476 AC: 19666 AN: 41354

American (AMR) AF: 0.265 AC: 4035 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3462

East Asian (EAS) AF: 0.353 AC: 1807 AN: 5112

South Asian (SAS) AF: 0.194 AC: 930 AN: 4788

European-Finnish (FIN) AF: 0.354 AC: 3730 AN: 10540

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19257 AN: 67876

Other (OTH) AF: 0.317 AC: 668 AN: 2104

Alfa AF: 0.315 Hom.: 972

Bravo AF: 0.344

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.16
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1993894; hg19: chr7-63817488;