rs3101793

Positions:

• chr10-26650472-A-G
• chr10-26650472-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026794.1(FAM238B):​n.5477-82A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 221,932 control chromosomes in the GnomAD database, including 8,641 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 0.26 (5743 hom., cov: 32)
  • Exomes 𝑓: 0.29 (2898 hom.)
• Consequence: FAM238B NR_026794.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM238B	NR_026794.1	n.5477-82A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000423917.5	n.601-82A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000413288.1	n.263-82A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000434458.5	n.387-82A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39961 AN: 151698 Hom.: 5739 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.285 AC: 20013 AN: 70116 Hom.: 2898 AF XY: 0.292 AC XY: 12070 AN XY: 41392

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.199

Gnomad4 ASJ exome AF: 0.287

Gnomad4 EAS exome AF: 0.335

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.329

Gnomad4 NFE exome AF: 0.311

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.263 AC: 39976 AN: 151816 Hom.: 5743 Cov.: 32 AF XY: 0.263 AC XY: 19505 AN XY: 74196

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.295

Alfa AF: 0.288 Hom.: 785

Bravo AF: 0.250

Asia WGS AF: 0.261 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.6
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3101793; hg19: chr10-26939401; COSMIC: COSV68899033;