chr4-68817077-G-A

Variant names:

• chr4-68817077-G-A
• rs7657958
• NM_001075.6:c.718+340G>A

Variant summary

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

The NM_001075.6(UGT2B10):​c.718+340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 151,690 control chromosomes in the GnomAD database, including 386 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 0.068 (386 hom., cov: 32)
• Consequence: UGT2B10 NM_001075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

UGT2B10 (HGNC:12544): (UDP glucuronosyltransferase family 2 member B10) Predicted to be involved in lipid metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.091 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.718+340G>A		intron_variant	Intron 1 of 5	ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.466+592G>A		intron_variant	Intron 1 of 5		NP_001138239.1
UGT2B10	NM_001290091.2	c.-27+905G>A		intron_variant	Intron 1 of 5		NP_001277020.1
UGT2B10	XM_017008585.3	c.718+340G>A		intron_variant	Intron 1 of 5		XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.718+340G>A		intron_variant	Intron 1 of 5	1	NM_001075.6	ENSP00000265403.7
UGT2B10	ENST00000458688.2	c.466+592G>A		intron_variant	Intron 1 of 5	2		ENSP00000413420.2

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10360 AN: 151572 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0683 AC: 10364 AN: 151690 Hom.: 386 Cov.: 32 AF XY: 0.0662 AC XY: 4908 AN XY: 74132

African (AFR) AF: 0.0443 AC: 1837 AN: 41446

American (AMR) AF: 0.0646 AC: 981 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 223 AN: 3456

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5170

South Asian (SAS) AF: 0.0352 AC: 169 AN: 4806

European-Finnish (FIN) AF: 0.0586 AC: 620 AN: 10584

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0929 AC: 6293 AN: 67744

Other (OTH) AF: 0.0719 AC: 151 AN: 2100

Alfa AF: 0.0683 Hom.: 113

Bravo AF: 0.0686

Asia WGS AF: 0.0180 AC: 64 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.47
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7657958; hg19: chr4-69682795;