rs78958330

Variant names:

• chr2-91893583-T-C
• rs78958330

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.000040 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00049 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC9B1P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 0 publications found

Genes affected

SLC9B1P2 (HGNC:37493): (solute carrier family 9 member B1 pseudogene 2)

ENSG00000290575 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9B1P2		n.91893583T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9B1P2	ENST00000398120.6	n.449-95A>G		intron_variant	Intron 3 of 7	6
ENSG00000290575	ENST00000606405.1	n.168-95A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0000404 AC: 6 AN: 148530 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000493

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000680

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000199

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000100

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000492

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000490 AC: 158 AN: 322544 Hom.: 0 AF XY: 0.000410 AC XY: 72 AN XY: 175552

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00108 AC: 9 AN: 8320

American (AMR) AF: 0.000670 AC: 8 AN: 11940

Ashkenazi Jewish (ASJ) AF: 0.000642 AC: 6 AN: 9346

East Asian (EAS) AF: 0.000653 AC: 15 AN: 22978

South Asian (SAS) AF: 0.000407 AC: 13 AN: 31926

European-Finnish (FIN) AF: 0.000206 AC: 4 AN: 19388

Middle Eastern (MID) AF: 0.00152 AC: 2 AN: 1320

European-Non Finnish (NFE) AF: 0.000477 AC: 95 AN: 199064

Other (OTH) AF: 0.000329 AC: 6 AN: 18262

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000404 AC: 6 AN: 148630 Hom.: 0 Cov.: 33 AF XY: 0.0000690 AC XY: 5 AN XY: 72476

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000492 AC: 2 AN: 40690

American (AMR) AF: 0.0000679 AC: 1 AN: 14722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3426

East Asian (EAS) AF: 0.000200 AC: 1 AN: 5006

South Asian (SAS) AF: 0.00 AC: 0 AN: 4640

European-Finnish (FIN) AF: 0.000100 AC: 1 AN: 9994

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 278

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66914

Other (OTH) AF: 0.000486 AC: 1 AN: 2058

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0158 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.70
DANN	Benign	0.53
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs78958330; hg19: chr2-92081609;