rs1000182

Positions:

• chr3-70321881-G-A
• chr3-70321881-G-T

Variant summary

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

The NR_186030.1(SAMMSON):​n.852+30638G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 151,960 control chromosomes in the GnomAD database, including 314 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 0.051 (314 hom., cov: 32)
• Consequence: SAMMSON NR_186030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

Genes affected

SAMMSON (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMMSON	NR_186030.1	n.852+30638G>A		intron_variant
SAMMSON	NR_186031.1	n.693-36373G>A		intron_variant
SAMMSON	NR_186032.1	n.837-36373G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000641222.1	n.615+19194G>A		intron_variant
SAMMSON	ENST00000642114.1	n.739+30638G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7724 AN: 151842 Hom.: 307 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.0581

Gnomad NFE AF: 0.0206

Gnomad OTH AF: 0.0396

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

GnomAD4 genome AF: 0.0511 AC: 7765 AN: 151960 Hom.: 314 Cov.: 32 AF XY: 0.0530 AC XY: 3935 AN XY: 74286

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.0101

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0206

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.0211 Hom.: 28

Bravo AF: 0.0488

Asia WGS AF: 0.0830 AC: 287 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1000182; hg19: chr3-70371032;