rs7657958

Positions:

• chr4-68817077-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.718+340G>A		intron_variant		ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.466+592G>A		intron_variant			NP_001138239.1
UGT2B10	NM_001290091.2	c.-27+905G>A		intron_variant			NP_001277020.1
UGT2B10	XM_017008585.3	c.718+340G>A		intron_variant			XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.718+340G>A		intron_variant		1	NM_001075.6	ENSP00000265403.7
UGT2B10	ENST00000458688.2	c.466+592G>A		intron_variant		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

Gnomad4 AFR AF: 0.0443

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0645

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0352

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0716 Hom.: 54

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7657958; hg19: chr4-69682795;