chr1-159721769-G-A

Variant names:

• chr1-159721769-G-A
• rs1341665
• ENST00000751816.1:n.108-4758G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-4758G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,958 control chromosomes in the GnomAD database, including 8,571 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 (8571 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 28 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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
ENSG00000297913	ENST00000751816.1	n.108-4758G>A		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-4758G>A		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-4758G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49270 AN: 151840 Hom.: 8563 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.324 AC: 49297 AN: 151958 Hom.: 8571 Cov.: 32 AF XY: 0.328 AC XY: 24397 AN XY: 74274

African (AFR) AF: 0.215 AC: 8896 AN: 41426

American (AMR) AF: 0.394 AC: 6012 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3130 AN: 5164

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4818

European-Finnish (FIN) AF: 0.383 AC: 4040 AN: 10542

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23271 AN: 67952

Other (OTH) AF: 0.345 AC: 728 AN: 2112

Alfa AF: 0.323 Hom.: 8036

Bravo AF: 0.321

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1341665; hg19: chr1-159691559;