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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841432.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309490	ENST00000841432.1		n.622-5710A>G		intron	N/A
	ENSG00000309490	ENST00000841433.1		n.619-1611A>G		intron	N/A
	ENSG00000309490	ENST00000841434.1		n.753-1611A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4750005;

hg19: chr10-6169685;