rs4948881

Variant names:

• chr10-44400587-T-C
• rs4948881
• XR_001747298.2:n.1967T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-44400587-T-C
• chr10-44400587-T-G

Variant summary

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

The XR_001747298.2(LOC107984179):​n.1967T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,154 control chromosomes in the GnomAD database, including 11,726 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 0.37 (11726 hom., cov: 32)
• Consequence: LOC107984179 XR_001747298.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 2 publications found

Genes affected

LOC107984179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984179	XR_001747298.2	n.1967T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303087	ENST00000791650.1	n.488-1122T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56086 AN: 152036 Hom.: 11718 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.369 AC: 56094 AN: 152154 Hom.: 11726 Cov.: 32 AF XY: 0.370 AC XY: 27531 AN XY: 74386

African (AFR) AF: 0.169 AC: 7000 AN: 41520

American (AMR) AF: 0.499 AC: 7631 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5174

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4814

European-Finnish (FIN) AF: 0.443 AC: 4684 AN: 10584

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31182 AN: 67986

Other (OTH) AF: 0.426 AC: 900 AN: 2114

Alfa AF: 0.436 Hom.: 24628

Bravo AF: 0.365

Asia WGS AF: 0.257 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.70
DANN	Benign	0.67
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4948881; hg19: chr10-44896035;