rs526847

Variant names:

• chr6-147915249-T-C
• rs526847
• XM_017010850.2:c.460-32223T>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

SAMD5 (HGNC:21180): (sterile alpha motif domain containing 5) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000227681 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427015.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227681	ENST00000427015.1	TSL:2	n.118-32223T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs526847;

hg19: chr6-148236385;