11-65827349-T-C

Position:

• chr11-65827349-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047427976.1(LOC124902693):​c.*598-740A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,144 control chromosomes in the GnomAD database, including 6,260 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 0.28 (6260 hom., cov: 33)
• Consequence: LOC124902693 XM_047427976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

Genes affected

LOC124902693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902693	XM_047427976.1	c.*598-740A>G		intron_variant			XP_047283932.1
LOC124902693	XM_047427977.1	c.*598-740A>G		intron_variant			XP_047283933.1
LOC124902693	XM_047427979.1	c.*598-227A>G		intron_variant			XP_047283935.1
LOC124902693	XM_047427980.1	c.*598-740A>G		intron_variant			XP_047283936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFL1	ENST00000525710.1	n.474-740A>G		intron_variant		5
CFL1	ENST00000527752.1	n.62-740A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42503 AN: 152026 Hom.: 6247 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.280 AC: 42551 AN: 152144 Hom.: 6260 Cov.: 33 AF XY: 0.272 AC XY: 20219 AN XY: 74392

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.283

Alfa AF: 0.326 Hom.: 13876

Bravo AF: 0.279

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7102454; hg19: chr11-65594820;