rs4750005

Variant names:

• chr10-6127722-T-C
• rs4750005
• ENST00000841432.1:n.622-5710A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000841432.1(ENSG00000309490):​n.622-5710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.14 (507 hom., cov: 0)
• Consequence: ENSG00000309490 ENST00000841432.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 9 publications found

Genes affected

ENSG00000309490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BS2: High Homozygotes in GnomAd4 at 507 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928080	XR_930619.3	n.615-1611A>G		intron_variant	Intron 1 of 2
LOC101928080	XR_930620.3	n.615-1639A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309490	ENST00000841432.1	n.622-5710A>G		intron_variant	Intron 1 of 1
ENSG00000309490	ENST00000841433.1	n.619-1611A>G		intron_variant	Intron 1 of 2
ENSG00000309490	ENST00000841434.1	n.753-1611A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 9603 AN: 70690 Hom.: 506 Cov.: 0

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.136 AC: 9618 AN: 70798 Hom.: 507 Cov.: 0 AF XY: 0.140 AC XY: 4935 AN XY: 35296

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.118 AC: 2754 AN: 23420

American (AMR) AF: 0.153 AC: 1079 AN: 7056

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 161 AN: 770

East Asian (EAS) AF: 0.0726 AC: 235 AN: 3238

South Asian (SAS) AF: 0.213 AC: 453 AN: 2130

European-Finnish (FIN) AF: 0.118 AC: 669 AN: 5686

Middle Eastern (MID) AF: 0.283 AC: 26 AN: 92

European-Non Finnish (NFE) AF: 0.148 AC: 4030 AN: 27168

Other (OTH) AF: 0.159 AC: 144 AN: 906

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.473 Hom.: 33411

Bravo AF: 0.426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	1.4
DANN	Benign	0.88
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs4750005; hg19: chr10-6169685;