chr6-148439903-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_015278.5(SASH1):​c.286-281G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,046 control chromosomes in the GnomAD database, including 13,772 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 13772 hom., cov: 32)

Consequence

SASH1
NM_015278.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.609
Variant links:
Genes affected
SASH1 (HGNC:19182): (SAM and SH3 domain containing 1) This gene encodes a scaffold protein involved in the TLR4 signaling pathway that may stimulate cytokine production and endothelial cell migration in response to invading pathogens. The encoded protein has also been described as a potential tumor suppressor that may negatively regulate proliferation, apoptosis, and invasion of cancer cells, and reduced expression of this gene has been observed in multiple human cancers. Mutations in this gene may be associated with abnormal skin pigmentation in human patients. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 6-148439903-G-T is Benign according to our data. Variant chr6-148439903-G-T is described in ClinVar as [Benign]. Clinvar id is 1288999.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SASH1NM_015278.5 linkuse as main transcriptc.286-281G>T intron_variant ENST00000367467.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SASH1ENST00000367467.8 linkuse as main transcriptc.286-281G>T intron_variant 1 NM_015278.5 P1
SASH1ENST00000367469.5 linkuse as main transcriptn.204-281G>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.422
AC:
64089
AN:
151928
Hom.:
13765
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.418
Gnomad AMI
AF:
0.454
Gnomad AMR
AF:
0.403
Gnomad ASJ
AF:
0.425
Gnomad EAS
AF:
0.414
Gnomad SAS
AF:
0.682
Gnomad FIN
AF:
0.454
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.406
Gnomad OTH
AF:
0.393
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.422
AC:
64126
AN:
152046
Hom.:
13772
Cov.:
32
AF XY:
0.430
AC XY:
31931
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.418
Gnomad4 AMR
AF:
0.403
Gnomad4 ASJ
AF:
0.425
Gnomad4 EAS
AF:
0.415
Gnomad4 SAS
AF:
0.682
Gnomad4 FIN
AF:
0.454
Gnomad4 NFE
AF:
0.406
Gnomad4 OTH
AF:
0.393
Alfa
AF:
0.494
Hom.:
1893

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.88
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10872615; hg19: chr6-148761039; API