rs912988

Variant names:

• chr1-5294784-C-T
• rs912988
• ENST00000819942.1:n.66-332G>A

Variant summary

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

The ENST00000819942.1(ENSG00000306645):​n.66-332G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,048 control chromosomes in the GnomAD database, including 8,270 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 (8270 hom., cov: 32)
• Consequence: ENSG00000306645 ENST00000819942.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 4 publications found

Genes affected

ENSG00000306645 (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 (NFE) allele frequency at 95% confidence interval = 0.383 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
ENSG00000306645	ENST00000819942.1	n.66-332G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48422 AN: 151930 Hom.: 8271 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.319 AC: 48434 AN: 152048 Hom.: 8270 Cov.: 32 AF XY: 0.319 AC XY: 23712 AN XY: 74330

African (AFR) AF: 0.210 AC: 8688 AN: 41466

American (AMR) AF: 0.333 AC: 5086 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3470

East Asian (EAS) AF: 0.132 AC: 680 AN: 5154

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4824

European-Finnish (FIN) AF: 0.406 AC: 4289 AN: 10566

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

European-Non Finnish (NFE) AF: 0.387 AC: 26312 AN: 67976

Other (OTH) AF: 0.330 AC: 697 AN: 2110

Alfa AF: 0.354 Hom.: 30032

Bravo AF: 0.306

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.55
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs912988; hg19: chr1-5354844;