6-147650438-C-T

Variant names:

• chr6-147650438-C-T
• rs1302019
• ENST00000566741.1:c.163-86879C>T

Variant summary

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

The ENST00000566741.1(SAMD5):​c.163-86879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 152,324 control chromosomes in the GnomAD database, including 71,697 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 0.97 (71697 hom., cov: 32)
• Consequence: SAMD5 ENST00000566741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372
• Publications: 9 publications found

Genes affected

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566741.1. 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
	SAMD5	ENST00000566741.1	TSL:3	c.163-86879C>T		intron	N/A	ENSP00000456528.1	H3BS43

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147637 AN: 152206 Hom.: 71641 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.968

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

GnomAD4 genome AF: 0.970 AC: 147753 AN: 152324 Hom.: 71697 Cov.: 32 AF XY: 0.968 AC XY: 72099 AN XY: 74476

African (AFR) AF: 0.980 AC: 40747 AN: 41572

American (AMR) AF: 0.974 AC: 14915 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.955 AC: 3317 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4604 AN: 5172

South Asian (SAS) AF: 0.977 AC: 4715 AN: 4826

European-Finnish (FIN) AF: 0.934 AC: 9915 AN: 10612

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66340 AN: 68042

Other (OTH) AF: 0.969 AC: 2050 AN: 2116

Alfa AF: 0.974 Hom.: 212241

Bravo AF: 0.973

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		0.37

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: rs1302019;

hg19: chr6-147971574;