chr7-33063693-A-C

Variant names:

• chr7-33063693-A-C
• rs34307182
• ENST00000788220.1:n.124+691A>C

Variant summary

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

The ENST00000788220.1(ENSG00000302625):​n.124+691A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,130 control chromosomes in the GnomAD database, including 7,375 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 0.30 (7375 hom., cov: 32)
• Consequence: ENSG00000302625 ENST00000788220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 publications found

Genes affected

ENSG00000302625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901610	XR_007060277.1	n.464+45A>C		intron_variant	Intron 1 of 4
LOC124901610	XR_007060278.1	n.464+45A>C		intron_variant	Intron 1 of 4
LOC124901610	XR_007060279.1	n.464+45A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302625	ENST00000788220.1	n.124+691A>C		intron_variant	Intron 1 of 2
ENSG00000302625	ENST00000788221.1	n.486+299A>C		intron_variant	Intron 1 of 2
ENSG00000302625	ENST00000788222.1	n.478+45A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46188 AN: 152012 Hom.: 7369 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.304 AC: 46217 AN: 152130 Hom.: 7375 Cov.: 32 AF XY: 0.306 AC XY: 22750 AN XY: 74362

African (AFR) AF: 0.226 AC: 9382 AN: 41504

American (AMR) AF: 0.419 AC: 6408 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1089 AN: 5180

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3675 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22393 AN: 67980

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.307 Hom.: 1050

Bravo AF: 0.307

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs34307182; hg19: chr7-33103305;