chr11-69371038-C-T

Variant names:

• chr11-69371038-C-T
• rs4275647
• XR_950269.4:n.4408C>T

Variant summary

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

The XR_950269.4(LOC105369370):​n.4408C>T 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 0.47 in 152,030 control chromosomes in the GnomAD database, including 17,935 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 0.47 (17935 hom., cov: 32)
• Consequence: LOC105369370 XR_950269.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 2 publications found

Genes affected

LOC105369370 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369370	XR_950269.4	n.4408C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260877	ENST00000561588.3	n.170-365C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71378 AN: 151912 Hom.: 17885 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.470 AC: 71496 AN: 152030 Hom.: 17935 Cov.: 32 AF XY: 0.464 AC XY: 34468 AN XY: 74318

African (AFR) AF: 0.658 AC: 27301 AN: 41490

American (AMR) AF: 0.485 AC: 7415 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1862 AN: 3462

East Asian (EAS) AF: 0.363 AC: 1869 AN: 5148

South Asian (SAS) AF: 0.249 AC: 1203 AN: 4824

European-Finnish (FIN) AF: 0.362 AC: 3830 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26539 AN: 67938

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.413 Hom.: 10033

Bravo AF: 0.494

Asia WGS AF: 0.351 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.83
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4275647; hg19: chr11-69185806;