rs646534

Variant names:

• chr1-54269065-G-A
• rs646534
• NM_145716.4:c.367-10916C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-54269065-G-A
• chr1-54269065-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145716.4(SSBP3):​c.367-10916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,926 control chromosomes in the GnomAD database, including 13,019 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 0.41 (13019 hom., cov: 32)
• Consequence: SSBP3 NM_145716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 3 publications found

Genes affected

SSBP3 (HGNC:15674): (single stranded DNA binding protein 3) Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in head development and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSBP3	NM_145716.4	c.367-10916C>T		intron_variant	Intron 5 of 17	ENST00000610401.6	NP_663768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6	c.367-10916C>T		intron_variant	Intron 5 of 17	5	NM_145716.4	ENSP00000479674.2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62431 AN: 151808 Hom.: 13006 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.411 AC: 62492 AN: 151926 Hom.: 13019 Cov.: 32 AF XY: 0.408 AC XY: 30268 AN XY: 74262

African (AFR) AF: 0.406 AC: 16822 AN: 41384

American (AMR) AF: 0.378 AC: 5761 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1225 AN: 5184

South Asian (SAS) AF: 0.482 AC: 2324 AN: 4826

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10562

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29967 AN: 67932

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.362 Hom.: 2528

Bravo AF: 0.404

Asia WGS AF: 0.409 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs646534; hg19: chr1-54734738;