rs10875423

Variant names:

• chr8-138289135-T-A
• rs10875423
• NM_015912.4:c.157+21706A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-138289135-T-A
• chr8-138289135-T-G

Variant summary

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

The ENST00000395297.6(FAM135B):​c.157+21706A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,118 control chromosomes in the GnomAD database, including 37,677 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 0.68 (37677 hom., cov: 33)
• Consequence: FAM135B ENST00000395297.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• Publications: 2 publications found

Genes affected

FAM135B (HGNC:28029): (family with sequence similarity 135 member B) Predicted to be involved in cellular lipid metabolic process. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000395297.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM135B	NM_015912.4	MANE Select	c.157+21706A>T		intron	N/A	NP_056996.2
	FAM135B	NM_001362965.2		c.157+21706A>T		intron	N/A	NP_001349894.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM135B	ENST00000395297.6	TSL:5 MANE Select	c.157+21706A>T		intron	N/A	ENSP00000378710.1
	FAM135B	ENST00000482951.6	TSL:1	n.*103+21706A>T		intron	N/A	ENSP00000429874.1
	FAM135B	ENST00000160713.8	TSL:3	c.157+21706A>T		intron	N/A	ENSP00000160713.4

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103793 AN: 152000 Hom.: 37679 Cov.: 33

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.683 AC: 103828 AN: 152118 Hom.: 37677 Cov.: 33 AF XY: 0.677 AC XY: 50363 AN XY: 74356

African (AFR) AF: 0.480 AC: 19894 AN: 41478

American (AMR) AF: 0.602 AC: 9190 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2706 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1437 AN: 5160

South Asian (SAS) AF: 0.810 AC: 3910 AN: 4826

European-Finnish (FIN) AF: 0.763 AC: 8079 AN: 10586

Middle Eastern (MID) AF: 0.772 AC: 224 AN: 290

European-Non Finnish (NFE) AF: 0.826 AC: 56157 AN: 68016

Other (OTH) AF: 0.713 AC: 1505 AN: 2110

Alfa AF: 0.750 Hom.: 5497

Bravo AF: 0.654

Asia WGS AF: 0.556 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		0.59
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: rs10875423; hg19: chr8-139301378;