rs3101793

Variant names:

• chr10-26650472-A-G
• rs3101793
• ENST00000413288.1:n.263-82A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000413288.1(ENSG00000290423):​n.263-82A>G variant causes a intron 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: ENSG00000290423 ENST00000413288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 1 publications found

Genes affected

ENSG00000290423 (HGNC:):

FAM238B (HGNC:44917): (family with sequence similarity 238 member B)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413288.1. 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
	FAM238B	NR_026794.1		n.5477-82A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290423	ENST00000413288.1	TSL:3	n.263-82A>G		intron	N/A
	ENSG00000290423	ENST00000423917.5	TSL:5	n.601-82A>G		intron	N/A
	ENSG00000290423	ENST00000434458.5	TSL:3	n.387-82A>G		intron	N/A

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

African (AFR) AF: 0.143 AC: 284 AN: 1984

American (AMR) AF: 0.199 AC: 1788 AN: 8986

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 296 AN: 1032

East Asian (EAS) AF: 0.335 AC: 1431 AN: 4272

South Asian (SAS) AF: 0.252 AC: 1954 AN: 7754

European-Finnish (FIN) AF: 0.329 AC: 1885 AN: 5732

Middle Eastern (MID) AF: 0.214 AC: 336 AN: 1570

European-Non Finnish (NFE) AF: 0.311 AC: 11186 AN: 35976

Other (OTH) AF: 0.304 AC: 853 AN: 2810

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

African (AFR) AF: 0.140 AC: 5811 AN: 41362

American (AMR) AF: 0.257 AC: 3919 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1041 AN: 3462

East Asian (EAS) AF: 0.336 AC: 1741 AN: 5174

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4802

European-Finnish (FIN) AF: 0.344 AC: 3625 AN: 10536

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21804 AN: 67922

Other (OTH) AF: 0.295 AC: 624 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.6
DANN	Benign	0.92
PhyloP100		0.23

Splicing

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

Other links and lift over

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