chr7-107802941-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000111.3(SLC26A3):​c.-89+170G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,042 control chromosomes in the GnomAD database, including 2,865 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 0.18 ( 2865 hom., cov: 31)

Consequence

SLC26A3
NM_000111.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.772
Variant links:
Genes affected
SLC26A3 (HGNC:3018): (solute carrier family 26 member 3) The protein encoded by this gene is a transmembrane glycoprotein that transports chloride ions across the cell membrane in exchange for bicarbonate ions. It is localized to the mucosa of the lower intestinal tract, particularly to the apical membrane of columnar epithelium and some goblet cells. The protein is essential for intestinal chloride absorption, and mutations in this gene have been associated with congenital chloride diarrhea. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC26A3NM_000111.3 linkuse as main transcriptc.-89+170G>A intron_variant ENST00000340010.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC26A3ENST00000340010.10 linkuse as main transcriptc.-89+170G>A intron_variant 1 NM_000111.3 P1
SLC26A3ENST00000453332.1 linkuse as main transcriptc.-89+181G>A intron_variant 4
SLC26A3ENST00000379083.7 linkuse as main transcriptc.-89+170G>A intron_variant, NMD_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.182
AC:
27633
AN:
151924
Hom.:
2861
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0898
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.244
Gnomad ASJ
AF:
0.128
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.260
Gnomad FIN
AF:
0.220
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.218
Gnomad OTH
AF:
0.201
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.182
AC:
27654
AN:
152042
Hom.:
2865
Cov.:
31
AF XY:
0.185
AC XY:
13746
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.0897
Gnomad4 AMR
AF:
0.245
Gnomad4 ASJ
AF:
0.128
Gnomad4 EAS
AF:
0.146
Gnomad4 SAS
AF:
0.259
Gnomad4 FIN
AF:
0.220
Gnomad4 NFE
AF:
0.218
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.213
Hom.:
504
Bravo
AF:
0.177
Asia WGS
AF:
0.212
AC:
736
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.60
DANN
Benign
0.30

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: rs4730268; hg19: chr7-107443386; API