GeneBe

chr3-70420625-T-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000641053.1(SAMMSON):​n.234-41935T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,146 control chromosomes in the GnomAD database, including 4,705 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 0.22 ( 4705 hom., cov: 33)

Consequence

SAMMSON
ENST00000641053.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119

Publications

2 publications found
Variant links:
Genes affected
SAMMSON (HGNC:49644): (survival associated mitochondrial melanoma specific oncogenic non-coding RNA)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SAMMSONNR_186031.1 linkn.764-9658T>A intron_variant Intron 6 of 6
SAMMSONNR_186032.1 linkn.908-9658T>A intron_variant Intron 8 of 8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SAMMSONENST00000641053.1 linkn.234-41935T>A intron_variant Intron 2 of 3
SAMMSONENST00000641222.1 linkn.687-4152T>A intron_variant Intron 5 of 5

Frequencies

GnomAD3 genomes
AF:
0.220
AC:
33440
AN:
152028
Hom.:
4706
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0699
Gnomad AMI
AF:
0.168
Gnomad AMR
AF:
0.197
Gnomad ASJ
AF:
0.241
Gnomad EAS
AF:
0.0406
Gnomad SAS
AF:
0.180
Gnomad FIN
AF:
0.250
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.243
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.220
AC:
33428
AN:
152146
Hom.:
4705
Cov.:
33
AF XY:
0.214
AC XY:
15917
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.0697
AC:
2893
AN:
41516
American (AMR)
AF:
0.197
AC:
3014
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.241
AC:
837
AN:
3468
East Asian (EAS)
AF:
0.0403
AC:
209
AN:
5180
South Asian (SAS)
AF:
0.181
AC:
874
AN:
4826
European-Finnish (FIN)
AF:
0.250
AC:
2640
AN:
10570
Middle Eastern (MID)
AF:
0.224
AC:
66
AN:
294
European-Non Finnish (NFE)
AF:
0.327
AC:
22237
AN:
67976
Other (OTH)
AF:
0.240
AC:
505
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1292
2584
3877
5169
6461
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
348
696
1044
1392
1740
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.271
Hom.:
775
Bravo
AF:
0.208
Asia WGS
AF:
0.102
AC:
354
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
4.5
DANN
Benign
0.81
PhyloP100
0.12

Splicing

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

Publications

Other links and lift over

dbSNP: rs1019374; hg19: chr3-70469776; API