rs7006742

Variant names:

• chr8-72324575-C-T
• rs7006742
• ENST00000803200.1:n.136-48158C>T

Variant summary

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

The ENST00000803200.1(ENSG00000304408):​n.136-48158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 152,032 control chromosomes in the GnomAD database, including 297 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 0.054 (297 hom., cov: 32)
• Consequence: ENSG00000304408 ENST00000803200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 2 publications found

Genes affected

ENSG00000304408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0922 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
ENSG00000304408	ENST00000803200.1	n.136-48158C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8230 AN: 151916 Hom.: 291 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0264

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0410

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0543 AC: 8256 AN: 152032 Hom.: 297 Cov.: 32 AF XY: 0.0539 AC XY: 4009 AN XY: 74326

African (AFR) AF: 0.0947 AC: 3925 AN: 41452

American (AMR) AF: 0.0583 AC: 890 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0475 AC: 165 AN: 3472

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5164

South Asian (SAS) AF: 0.0262 AC: 126 AN: 4808

European-Finnish (FIN) AF: 0.0176 AC: 186 AN: 10588

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0410 AC: 2788 AN: 67980

Other (OTH) AF: 0.0645 AC: 136 AN: 2108

Alfa AF: 0.0497 Hom.: 42

Bravo AF: 0.0574

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.55
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7006742; hg19: chr8-73236810;