rs7750345

Variant names:

• chr6-105812253-A-G
• rs7750345
• ENST00000644129.1:n.281+17804T>C

Variant summary

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

The ENST00000644129.1(ENSG00000284999):​n.281+17804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,816 control chromosomes in the GnomAD database, including 7,377 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 (7377 hom., cov: 31)
• Consequence: ENSG00000284999 ENST00000644129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 7 publications found

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.415 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
ENSG00000284999	ENST00000644129.1	n.281+17804T>C		intron_variant	Intron 3 of 3
ENSG00000284999	ENST00000744159.1	n.374+17804T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45566 AN: 151698 Hom.: 7364 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.300 AC: 45620 AN: 151816 Hom.: 7377 Cov.: 31 AF XY: 0.299 AC XY: 22196 AN XY: 74182

African (AFR) AF: 0.420 AC: 17375 AN: 41358

American (AMR) AF: 0.227 AC: 3457 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 907 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1146 AN: 5128

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3059 AN: 10536

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17537 AN: 67936

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.317 Hom.: 3144

Bravo AF: 0.301

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs7750345; hg19: chr6-106260128;