chr1-23954616-C-T

Variant names:

• chr1-23954616-C-T
• rs7530595
• ENST00000761346.1:n.130+4307G>A

Variant summary

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

The ENST00000761346.1(ENSG00000299163):​n.130+4307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,876 control chromosomes in the GnomAD database, including 9,286 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 (9286 hom., cov: 31)
• Consequence: ENSG00000299163 ENST00000761346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• Publications: 3 publications found

Genes affected

ENSG00000299163 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903877	XR_007065541.1	n.17-1540G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299163	ENST00000761346.1	n.130+4307G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48264 AN: 151758 Hom.: 9278 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.318 AC: 48282 AN: 151876 Hom.: 9286 Cov.: 31 AF XY: 0.316 AC XY: 23431 AN XY: 74212

African (AFR) AF: 0.102 AC: 4226 AN: 41430

American (AMR) AF: 0.288 AC: 4386 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5162

South Asian (SAS) AF: 0.251 AC: 1206 AN: 4810

European-Finnish (FIN) AF: 0.469 AC: 4935 AN: 10514

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29135 AN: 67920

Other (OTH) AF: 0.325 AC: 686 AN: 2110

Alfa AF: 0.376 Hom.: 12430

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.92
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7530595; hg19: chr1-24281106;