7-75722-C-T

Variant names:

• chr7-75722-C-T
• rs10233991
• ENST00000465755.2:n.121-3889G>A

Variant summary

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

The ENST00000465755.2(ENSG00000287883):​n.121-3889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 150,716 control chromosomes in the GnomAD database, including 3,614 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 0.28 (3614 hom., cov: 33)
• Consequence: ENSG00000287883 ENST00000465755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 1 publications found

Genes affected

ENSG00000287883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375113	NR_187845.1	n.50-26G>A		intron_variant	Intron 1 of 3
LOC105375113	NR_187846.1	n.50-3889G>A		intron_variant	Intron 1 of 2
LOC105375113	NR_187847.1	n.50-26G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287883	ENST00000465755.2	n.121-3889G>A		intron_variant	Intron 1 of 2	3
ENSG00000287883	ENST00000821341.1	n.390-26G>A		intron_variant	Intron 2 of 3
ENSG00000287883	ENST00000850640.1	n.448-2460G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42689 AN: 150614 Hom.: 3614 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.283 AC: 42700 AN: 150716 Hom.: 3614 Cov.: 33 AF XY: 0.284 AC XY: 20898 AN XY: 73682

African (AFR) AF: 0.170 AC: 7004 AN: 41090

American (AMR) AF: 0.335 AC: 5069 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1238 AN: 3436

East Asian (EAS) AF: 0.138 AC: 711 AN: 5144

South Asian (SAS) AF: 0.297 AC: 1420 AN: 4778

European-Finnish (FIN) AF: 0.315 AC: 3309 AN: 10518

Middle Eastern (MID) AF: 0.365 AC: 105 AN: 288

European-Non Finnish (NFE) AF: 0.342 AC: 23000 AN: 67346

Other (OTH) AF: 0.306 AC: 641 AN: 2096

Alfa AF: 0.178 Hom.: 208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs10233991; hg19: chr7-75722;