7-30911127-G-C

Variant names:

• chr7-30911127-G-C
• rs1476597
• ENST00000509504.2:c.621-866G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509504.2(ENSG00000250424):​c.621-866G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,900 control chromosomes in the GnomAD database, including 27,800 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 0.57 (27800 hom., cov: 33)
• Consequence: ENSG00000250424 ENST00000509504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

ENSG00000250424 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.865 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.621-866G>C		intron_variant	Intron 7 of 10	5		ENSP00000421315.2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87223 AN: 151784 Hom.: 27753 Cov.: 33

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.575 AC: 87324 AN: 151900 Hom.: 27800 Cov.: 33 AF XY: 0.570 AC XY: 42308 AN XY: 74208

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.547

Alfa AF: 0.351 Hom.: 974

Bravo AF: 0.592

Asia WGS AF: 0.447 AC: 1558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.25

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476597; hg19: chr7-30950742;