ENST00000427015.1:n.118-32223T>C

Variant names:

• chr6-147915249-T-C
• rs526847
• ENST00000427015.1:n.118-32223T>C

Variant summary

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

The ENST00000427015.1(ENSG00000227681):​n.118-32223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,980 control chromosomes in the GnomAD database, including 21,300 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 0.51 (21300 hom., cov: 31)
• Consequence: ENSG00000227681 ENST00000427015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 6 publications found

Genes affected

ENSG00000227681 (HGNC:):

SAMD5 (HGNC:21180): (sterile alpha motif domain containing 5) Located in cytoplasm. [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 (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD5	XM_017010850.2	c.460-32223T>C		intron_variant	Intron 1 of 1		XP_016866339.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227681	ENST00000427015.1	n.118-32223T>C		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76724 AN: 151862 Hom.: 21259 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.506 AC: 76832 AN: 151980 Hom.: 21300 Cov.: 31 AF XY: 0.505 AC XY: 37537 AN XY: 74290

African (AFR) AF: 0.748 AC: 30996 AN: 41448

American (AMR) AF: 0.495 AC: 7561 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1178 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2651 AN: 5166

South Asian (SAS) AF: 0.553 AC: 2664 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3785 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26665 AN: 67958

Other (OTH) AF: 0.470 AC: 989 AN: 2104

Alfa AF: 0.426 Hom.: 17023

Bravo AF: 0.525

Asia WGS AF: 0.550 AC: 1909 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs526847; hg19: chr6-148236385;