chr3-70011930-A-G

Position:

• chr3-70011930-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000483525.2(SAMMSON):​n.136-427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 152,194 control chromosomes in the GnomAD database, including 52 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 0.019 (52 hom., cov: 31)
• Consequence: SAMMSON ENST00000483525.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

SAMMSON (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0186 (2826/152194) while in subpopulation AFR AF= 0.036 (1493/41504). AF 95% confidence interval is 0.0345. There are 52 homozygotes in gnomad4. There are 1404 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMMSON	NR_110000.2	n.136-427A>G		intron_variant
SAMMSON	NR_186009.1	n.34-427A>G		intron_variant
SAMMSON	NR_186010.1	n.136-427A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000483525.2	n.136-427A>G		intron_variant		1
SAMMSON	ENST00000488861.7	n.56-427A>G		intron_variant		3
SAMMSON	ENST00000641005.1	n.243-427A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0185 AC: 2815 AN: 152078 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0135

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.00575

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0186 AC: 2826 AN: 152194 Hom.: 52 Cov.: 31 AF XY: 0.0189 AC XY: 1404 AN XY: 74398

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.0135

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.0132

Gnomad4 SAS AF: 0.0349

Gnomad4 FIN AF: 0.00575

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0128 Hom.: 2

Bravo AF: 0.0193

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
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: rs10510993; hg19: chr3-70061081;