7-30897563-T-C

Variant names:

• chr7-30897563-T-C
• rs1000597
• ENST00000509504.2:c.621-14430T>C

Variant summary

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

The ENST00000509504.2(ENSG00000250424):​c.621-14430T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,148 control chromosomes in the GnomAD database, including 1,536 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 0.12 (1536 hom., cov: 32)
• Consequence: ENSG00000250424 ENST00000509504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 23 publications found

Genes affected

ENSG00000250424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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
ENSG00000250424	ENST00000509504.2	c.621-14430T>C		intron_variant	Intron 7 of 10	5		ENSP00000421315.2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18730 AN: 152030 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.123 AC: 18788 AN: 152148 Hom.: 1536 Cov.: 32 AF XY: 0.122 AC XY: 9078 AN XY: 74394

African (AFR) AF: 0.223 AC: 9269 AN: 41500

American (AMR) AF: 0.0726 AC: 1111 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.145 AC: 750 AN: 5156

South Asian (SAS) AF: 0.162 AC: 781 AN: 4808

European-Finnish (FIN) AF: 0.0734 AC: 778 AN: 10594

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.0785 AC: 5336 AN: 68010

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.0912 Hom.: 2970

Bravo AF: 0.125

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.31
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1000597; hg19: chr7-30937178;