rs654657

Positions:

• chr6-147913308-A-C
• chr6-147913308-A-T

Variant summary

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

The ENST00000427015.1(ENSG00000227681):​n.118-34164A>C 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 0.589 in 152,012 control chromosomes in the GnomAD database, including 27,238 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 0.59 (27238 hom., cov: 32)
• Consequence: ENST00000427015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD5	XM_017010850.2	c.460-34164A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000427015.1	n.118-34164A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89478 AN: 151894 Hom.: 27191 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.589 AC: 89587 AN: 152012 Hom.: 27238 Cov.: 32 AF XY: 0.590 AC XY: 43817 AN XY: 74282

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.555

Alfa AF: 0.399 Hom.: 950

Bravo AF: 0.601

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs654657; hg19: chr6-148234444;